Inhibitors of cyclindependent kinase 7 (cdk7)

ABSTRACT

The present invention provides novel compounds of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof. Also provided are methods and kits involving the inventive compounds or compositions for treating and/or preventing proliferative diseases (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt&#39;s lymphoma, melanoma, multiple myeloma, breast cancer, Ewing&#39;s sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject. Treatment of a subject with a proliferative disease using a compound or composition of the invention may inhibit the aberrant activity of a kinase, such as a cyclin-dependent kinase (CDK) (e.g., cyclin-dependent kinase 7 (CDK7)), and therefore, induce cellular apoptosis and/or inhibit transcription in the subject.

RELATED APPLICATIONS

This application claims priority under 35 U.S.C. § 119(e) to U.S.Provisional Application Ser. No. 62/096,040, filed Dec. 23, 2014, theentire contents of which are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under grant number 1 R01CA 179483-01A1 awarded by the National Institutes of Health. Thegovernment has certain rights in the invention.

BACKGROUND OF THE INVENTION

The members of the cyclin-dependent kinase (CDK) family play criticalregulatory roles in cell proliferation. There are currently 20 knownmammalian CDKs. While CDK7-CDK13 have been linked to transcription, onlyCDK1, 2, 4, and 6 show demonstrable association with the cell cycle.Unique among the mammalian CDKs, CDK7 has consolidated kinaseactivities, regulating both the cell cycle and transcription. In thecytosol, CDK7 exists as a heterotrimeric complex and is believed tofunction as a CDK1/2-activating kinase (CAK), whereby phosphorylation ofconserved residues in CDK1/2 by CDK7 is required for full catalytic CDKactivity and cell cycle progression (Desai et al., “Effects ofphosphorylation by CAK on cyclin binding by CDC2 and CDK2.” Mol. CellBiol. 15, 345-350 (1995); Kaldis et al., “Analysis of CAK activitiesfrom human cells.” Eur. J. Biochem. 267, 4213-4221 (2000); Larochelle etal., “Requirements for CDK7 in the assembly of CDK1/cyclin B andactivation of CDK2 revealed by chemical genetics in human cells.” Mol.Cell 25, 839-850 (2007)). In the nucleus, CDK7 forms the kinase core ofthe RNA polymerase (RNAP) II general transcription factor complex and ischarged with phosphorylating the C-terminal domain (CTD) of RNAP II, arequisite step in gene transcriptional initiation (Serizawa. et al.,“Association of CDK-activating kinase subunits with transcription factorTFIIH.” Nature 374, 280-282 (1995); Shiekhattar et al., “CDK-activatingkinase complex is a component of human transcription factor TFIIH.”Nature 374, 283-287 (1995); Drapkin et al., “Human cyclin-dependentkinase-activating kinase exists in three distinct complexes.” Proc.Natl. Acad. Sci. U.S.A. 93, 6488-6493 (1996); Liu. et al., “Twocyclin-dependent kinases promote RNA polymerase II transcription andformation of the scaffold complex.” Mol. Cell Biol. 24, 1721-1735(2004); Akhtar et al., “TFIIH kinase places bivalent marks on thecarboxy-terminal domain of RNA polymerase II.” Mol. Cell 34, 387-393(2009); Glover-Cutter et al., “TFIIH-associated CDK7 kinase functions inphosphorylation of C-terminal domain Ser7 residues, promoter-proximalpausing, and termination by RNA polymerase II.” Mol. Cell Biol. 29,5455-5464 (2009)). Together, the two functions of CDK7, i.e., CAK andCTD phosphorylation, support critical facets of cellular proliferation,cell cycling, and transcription.

Disruption of RNAP II CTD phosphorylation has been shown topreferentially affect proteins with short half-lives, including those ofthe anti-apoptotic BCL-2 family (Konig et al., “The novelcyclin-dependent kinase inhibitor flavopiridol downregulates Bcl-2 andinduces growth arrest and apoptosis in chronic B-cell leukemia lines.”Blood 1, 4307-4312 (1997); Gojo et al., “The cyclin-dependent kinaseinhibitor flavopiridol induces apoptosis in multiple myeloma cellsthrough transcriptional repression and down-regulation of Mcl-1.” Clin.Cancer Res. 8, 3527-3538 (2002)). Cancer cells have demonstrated abilityto circumvent pro-cell death signaling through up-regulation of BCL-2family members (Llambi et al., “Apoptosis and oncogenesis: give and takein the BCL-2 family.” Curr. Opin. Genet. Dev. 21, 12-20 (2011)).Therefore, inhibition of human CDK7 kinase activity is likely to resultin anti-proliferative activity, and pharmacological inhibition isthought to be useful in treating proliferative disorders, includingcancer. Indeed, flavopiridol, a non-selective pan-CDK inhibitor thattargets CTD kinases, has demonstrated efficacy for the treatment ofchronic lymphocytic leukemia (CLL) but suffers from a poor toxicityprofile (Lin et al., “Phase II study of flavopiridol in relapsed chroniclymphocytic leukemia demonstrating high response rates in geneticallyhigh-risk disease.” J. Clin. Oncol. 27, 6012-6018 (2009); Christian etal., “Flavopiridol in chronic lymphocytic leukemia: a concise review.”Clin. Lymphoma Myeloma 9 Suppl. 3, S179-S185 (2009)). A selective CDK7inhibitor may hold promise as a therapeutic agent for the treatment ofCLL and other cancers.

SUMMARY OF THE INVENTION

The present invention provides compounds of Formula (I), andpharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,prodrugs, and compositions thereof. The compounds of Formula (I), andpharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,prodrugs, and compositions thereof, may inhibit the activity of akinase. In certain embodiments, the inhibited kinase is a CDK. Incertain embodiments, the kinase is CDK7. In certain embodiments, thecompound of Formula (I) is selective for CDK7 compared to other kinases(e.g., CDK12 and CDK13). The present invention further provides methodsof using the inventive compounds, and pharmaceutically acceptable salts,solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers,isotopically labeled derivatives, prodrugs, and compositions thereof, tostudy the inhibition of a kinase (e.g., CDK7) and as therapeutics forthe prevention and/or treatment of diseases associated with theoverexpression and/or aberrant activity of a kinase (e.g., CDK7). Incertain embodiments, the inventive compounds are used for the preventionand/or treatment of proliferative diseases (e.g., cancers (e.g.,leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma,melanoma, multiple myeloma, breast cancer, Ewing's sarcoma,osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectalcancer), benign neoplasms, diseases associated with angiogenesis,inflammatory diseases, autoinflammatory diseases, and autoimmunediseases) in a subject.

In certain embodiments, the compounds of Formula (I) may selectivelyinhibit the activity of CDK7 compared to CDK13. Since the discovery ofselective inhibitors of CDK7 has been hampered by the high sequence andstructural similarities of the kinase domain of CDK family members, thedevelopment of selective inhibitors of the transcriptionalcyclin-dependent kinases (tCDKs) will allow dissection of theirindividual contributions to the regulation of transcription andevaluation of their therapeutic potential. Without wishing to be boundby any particular theory, the inventive compounds' selectivity for CDK7may be due to the compounds' ability to covalently modify the cysteineresidue (Cys312) of CDK7. Cys312 of CDK7 is largely unique among theCDKs and other kinases.

In one aspect, the present invention provides compounds of Formula (I):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein R¹, R², R³, R⁴, R⁵, linker L¹, linker L²,Ring A, and Ring B are as defined herein.

In certain embodiments, a compound of Formula (I) is of Formula (II):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L², Ring A, and Ring B are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula (III):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L², Ring A, and Ring B are asdefined herein.

In certain embodiments, a compound of Formula (I) is of Formula (V-a),(V-b), (V-c), or (V-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R², R^(1a), R^(1N), R^(2N), linker L², Ring A,and Ring B are as defined herein.

In certain embodiments, a compound of Formula (I) is of Formula (IX-a),(IX-b), (IX-C), or (IX-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, linker L², Ring A, and Ring B are asdefined herein.

In another aspect, the present disclosure provides pharmaceuticalcompositions including a compound described herein, and optionally apharmaceutically acceptable excipient. In certain embodiments, thepharmaceutical compositions described herein include a therapeuticallyor prophylactically effective amount of a compound described herein. Thepharmaceutical composition may be useful for treating a proliferativedisease in a subject in need thereof, preventing a proliferative diseasein a subject in need thereof, inhibiting the activity of a proteinkinase in a subject, biological sample, tissue, or cell, and/or inducingapoptosis in a cell.

In another aspect, the present invention provides methods for treatingand/or preventing a proliferative disease. Exemplary proliferativediseases which may be treated include cancer (e.g., leukemia, acutelymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiplemyeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer,neuroblastoma, lung cancer, colorectal cancer), benign neoplasm,diseases associated with angiogenesis, inflammatory diseases,autoinflammatory diseases, and autoimmune diseases.

Another aspect of the invention relates to methods of inhibiting theactivity of a kinase (e.g., CDK (e.g., CDK7)) in a biological sample orsubject. In certain embodiments, the method involves the selectiveinhibition of CDK7.

Also provided by the present invention are methods of inhibitingtranscription in a biological sample or subject. The transcription ofgenes affected by the activity of CDK7 may be inhibited by the compoundsof the invention.

The present invention also provides methods of inhibiting cell growth ina biological sample or subject. In still another aspect, the presentinvention provides methods of inducing apoptosis of a cell in abiological sample or a subject.

In yet another aspect, the present invention provides compounds ofFormula (I), and pharmaceutically acceptable salts, solvates, hydrates,polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeledderivatives, prodrugs, and compositions thereof, for use in thetreatment of a proliferative disease (e.g., cancer) in a subject.

Another aspect of the present disclosure relates to kits comprising acontainer with a compound, or pharmaceutical composition thereof, asdescribed herein. The kits described herein may include a single dose ormultiple doses of the compound or pharmaceutical composition. The kitsmay be useful in a method of the disclosure. In certain embodiments, thekit further includes instructions for using the compound orpharmaceutical composition. A kit described herein may also includeinformation (e.g. prescribing information) as required by a regulatoryagency such as the U.S. Food and Drug Administration (FDA).

The present invention describes methods for administering to the subjectan effective amount of a compound, or pharmaceutical compositionthereof, as described herein. Also described are methods for a cell withan effective amount of a compound, or pharmaceutical compositionthereof, as described herein. In certain embodiments, a method describedherein further includes administering to the subject an additionalpharmaceutical agent. In certain embodiments, a method described hereinfurther includes contacting the cell with an additional pharmaceuticalagent. A method described herein may further include performingradiotherapy, immunotherapy, and/or transplantation on the subject.

In yet another aspect, the present disclosure provides compounds, andpharmaceutical compositions thereof, as described herein for use in amethod of the disclosure.

The details of one or more embodiments of the invention are set forthherein. Other features, objects, and advantages of the invention will beapparent from the Detailed Description, the Examples, and the Claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawing, which are incorporated in and constitute apart of this specification, illustrate several embodiments of theinvention and together with the description, serve to explain theprinciples of the invention.

FIG. 1 shows the total ion chromatograms (TIC; A,E) and extracted ionchromatograms (XIC; B-D, F-H) for CDK7 peptides recorded during analysisof CAK complexes treated with DMSO (A-D) or Compound 101 (E-H). FIG. 1A:TIC; DMSO. FIG. 1B: XIC; DMSO. FIG. 1C: XIC; DMSO. FIG. 1D: XIC; DMSO.FIG. 1E: TIC; compound 101. FIG. 1F: XIC; compound 101. FIG. 1G: XIC;compound 101. FIG. 1H: XIC; compound 101.

FIG. 2 shows an MS spectrum (m/z 686-690) recorded during analysis ofpeptides derived from CDK7 treated with Compound 101. Signal at m/z687.7498 corresponds to YFSNRPGPTPGCQLPRPNCPVETLK, with Cys312 labeledwith Compound 101.

DEFINITIONS

Definitions of specific functional groups and chemical terms aredescribed in more detail below. The chemical elements are identified inaccordance with the Periodic Table of the Elements, CAS version,Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, andspecific functional groups are generally defined as described therein.Additionally, general principles of organic chemistry, as well asspecific functional moieties and reactivity, are described in ThomasSorrell, Organic Chemistry, University Science Books, Sausalito, 1999;Smith and March, March's Advanced Organic Chemistry, 5^(th) Edition,John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive OrganicTransformations, VCH Publishers, Inc., New York, 1989; and Carruthers,Some Modern Methods of Organic Synthesis, 3^(rd) Edition, CambridgeUniversity Press, Cambridge, 1987. The disclosure is not intended to belimited in any manner by the exemplary listing of substituents describedherein.

Compounds described herein can comprise one or more asymmetric centers,and thus can exist in various isomeric forms, e.g., enantiomers and/ordiastereomers. For example, the compounds described herein can be in theform of an individual enantiomer, diastereomer or geometric isomer, orcan be in the form of a mixture of stereoisomers, including racemicmixtures and mixtures enriched in one or more stereoisomer. Isomers canbe isolated from mixtures by methods known to those skilled in the art,including chiral high pressure liquid chromatography (HPLC) and theformation and crystallization of chiral salts; or preferred isomers canbe prepared by asymmetric syntheses. See, for example, Jacques et al.,Enantiomers, Racemates and Resolutions (Wiley Interscience, New York,1981); Wilen et Tetrahedron 33:2725 (1977); Eliel, Stereochemistry ofCarbon Compounds (McGraw-Hill, N Y, 1962); and Wilen, Tables ofResolving Agents and Optical Resolutions p. 268 (E.L. Ed., Univ. ofNotre Dame Press, Notre Dame, Ind. 1972). The disclosure additionallyencompasses compounds described herein as individual isomerssubstantially free of other isomers, and alternatively, as mixtures ofvarious isomers.

When a range of values is listed, it is intended to encompass each valueand sub-range within the range. For example “C₁₋₆” is intended toencompass, C₁, C₂, C₃, C₄, C₅, C₆, C₁₋₆, C₁₋₅, C₁₋₄, C₁₋₃, C₁₋₂, C₂₋₆,C₂₋₅, C₂₋₄, C₂₋₃, C₃₋₆, C₃₋₅, C₃₋₄, C₄₋₆, C₄₋₅, and C₅₋₆.

The term “aliphatic” includes both saturated and unsaturated, straightchain (i.e., unbranched), branched, acyclic, cyclic, or polycyclicaliphatic hydrocarbons, which are optionally substituted with one ormore functional groups. As will be appreciated by one of ordinary skillin the art, “aliphatic” is intended herein to include, but is notlimited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, andcycloalkynyl moieties. Thus, the term “alkyl” includes straight,branched and cyclic alkyl groups. An analogous convention applies toother generic terms such as “alkenyl”, “alkynyl”, and the like.Furthermore, the terms “alkyl”, “alkenyl”, “alkynyl”, and the likeencompass both substituted and unsubstituted groups. In certainembodiments, “lower alkyl” is used to indicate those alkyl groups(cyclic, acyclic, substituted, unsubstituted, branched or unbranched)having 1-6 carbon atoms.

In certain embodiments, the alkyl, alkenyl, and alkynyl groups employedin the disclosure contain 1-20 aliphatic carbon atoms. In certain otherembodiments, the alkyl, alkenyl, and alkynyl groups employed in thedisclosure contain 1-10 aliphatic carbon atoms. In yet otherembodiments, the alkyl, alkenyl, and alkynyl groups employed in thedisclosure contain 1-8 aliphatic carbon atoms. In still otherembodiments, the alkyl, alkenyl, and alkynyl groups employed in thedisclosure contain 1-6 aliphatic carbon atoms. In yet other embodiments,the alkyl, alkenyl, and alkynyl groups employed in the disclosurecontain 1-4 carbon atoms. Illustrative aliphatic groups thus include,but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl,cyclopropyl, —CH₂-cyclopropyl, vinyl, allyl, n-butyl, sec-butyl,isobutyl, tert-butyl, cyclobutyl, —CH₂-cyclobutyl, n-pentyl, sec-pentyl,isopentyl, tert-pentyl, cyclopentyl, —CH₂-cyclopentyl, n-hexyl,sec-hexyl, cyclohexyl, —CH₂-cyclohexyl moieties and the like, whichagain, may bear one or more substituents. Alkenyl groups include, butare not limited to, for example, ethenyl, propenyl, butenyl,1-methyl-2-buten-1-yl, and the like. Representative alkynyl groupsinclude, but are not limited to, ethynyl, 2-propynyl (propargyl),1-propynyl, and the like.

The term “alkyl” refers to a radical of a straight-chain or branchedsaturated hydrocarbon group having from 1 to 10 carbon atoms (“C₁₋₁₀alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms(“C₁₋₉ alkyl”). In some embodiments, an alkyl group has 1 to 8 carbonatoms (“C₁₋₈ alkyl”). In some embodiments, an alkyl group has 1 to 7carbon atoms (“C₁₋₇ alkyl”). In some embodiments, an alkyl group has 1to 6 carbon atoms (“C₁₋₆ alkyl”). In some embodiments, an alkyl grouphas 1 to 5 carbon atoms (“C₁₋₅ alkyl”). In some embodiments, an alkylgroup has 1 to 4 carbon atoms (“C₁₋₄ alkyl”). In some embodiments, analkyl group has 1 to 3 carbon atoms (“C₁₋₃ alkyl”). In some embodiments,an alkyl group has 1 to 2 carbon atoms (“C₁₋₂ alkyl”). In someembodiments, an alkyl group has 1 carbon atom (“C₁ alkyl”). In someembodiments, an alkyl group has 2 to 6 carbon atoms (“C₂₋₆ alkyl”).Examples of C₁₋₆ alkyl groups include methyl (C₁), ethyl (C₂), propyl(C₃) (e.g., n-propyl, isopropyl), butyl (C₄) (e.g., n-butyl, tert-butyl,sec-butyl, iso-butyl), pentyl (C₅) (e.g., n-pentyl, 3-pentanyl, amyl,neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (C₆) (e.g.,n-hexyl). Additional examples of alkyl groups include n-heptyl (C₇),n-octyl (C₈), and the like. Unless otherwise specified, each instance ofan alkyl group is independently unsubstituted (an “unsubstituted alkyl”)or substituted (a “substituted alkyl”) with one or more substituents(e.g., halogen, such as F). In certain embodiments, the alkyl group isan unsubstituted C₁₋₁₀ alkyl (such as unsubstituted C₁₋₆ alkyl, e.g.,—CH₃). In certain embodiments, the alkyl group is a substituted C₁₋₁₀alkyl (such as substituted C₁₋₆ alkyl, e.g., —CF₃).

“Alkenyl” refers to a radical of a straight-chain or branchedhydrocarbon group having from 2 to 20 carbon atoms, one or morecarbon-carbon double bonds, and no triple bonds (“C₂₋₂₀ alkenyl”). Insome embodiments, an alkenyl group has 2 to 10 carbon atoms (“C₂₋₁₀alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms(“C₂₋₉ alkenyl”). In some embodiments, an alkenyl group has 2 to 8carbon atoms (“C₂₋₈ alkenyl”). In some embodiments, an alkenyl group has2 to 7 carbon atoms (“C₂₋₇ alkenyl”). In some embodiments, an alkenylgroup has 2 to 6 carbon atoms (“C₂₋₆ alkenyl”). In some embodiments, analkenyl group has 2 to 5 carbon atoms (“C₂₋₅ alkenyl”). In someembodiments, an alkenyl group has 2 to 4 carbon atoms (“C₂₋₄ alkenyl”).In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C₂₋₃alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C₂alkenyl”). The one or more carbon-carbon double bonds can be internal(such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples ofC₂₋₄ alkenyl groups include ethenyl (C₂), 1-propenyl (C₃), 2-propenyl(C₃), 1-butenyl (C₄), 2-butenyl (C₄), butadienyl (C₄), and the like.Examples of C₂₋₆ alkenyl groups include the aforementioned C₂₋₄ alkenylgroups as well as pentenyl (C₅), pentadienyl (C₅), hexenyl (C₆), and thelike. Additional examples of alkenyl include heptenyl (C₇), octenyloctatrienyl (C₈), and the like. Unless otherwise specified, eachinstance of an alkenyl group is independently optionally substituted,i.e., unsubstituted (an “unsubstituted alkenyl”) or substituted (a“substituted alkenyl”) with one or more substituents. In certainembodiments, the alkenyl group is unsubstituted C₂₋₁₀ alkenyl. Incertain embodiments, the alkenyl group is substituted C₂₋₁₀ alkenyl. Inan alkenyl group, a C═C double bond for which the stereochemistry is notspecified (e.g., —CH═CHCH₃ or

may be an (E)- or (Z)-double bond.

“Alkynyl” refers to a radical of a straight-chain or branchedhydrocarbon group having from 2 to 20 carbon atoms, one or morecarbon-carbon triple bonds, and optionally one or more double bonds(“C₂₋₂₀ alkynyl”). In some embodiments, an alkynyl group has 2 to 10carbon atoms (“C₂₋₁₀ alkynyl”). In some embodiments, an alkynyl grouphas 2 to 9 carbon atoms (“C₂₋₉ alkynyl”). In some embodiments, analkynyl group has 2 to 8 carbon atoms (“C₂₋₈ alkynyl”). In someembodiments, an alkynyl group has 2 to 7 carbon atoms (“C₂₋₇ alkynyl”).In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C₂₋₆alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms(“C₂₋₅ alkynyl”). In some embodiments, an alkynyl group has 2 to 4carbon atoms (“C₂₋₄ alkynyl”). In some embodiments, an alkynyl group has2 to 3 carbon atoms (“C₂₋₃ alkynyl”). In some embodiments, an alkynylgroup has 2 carbon atoms (“C₂ alkynyl”). The one or more carbon-carbontriple bonds can be internal (such as in 2-butynyl) or terminal (such asin 1-butynyl). Examples of C₂₋₄ alkynyl groups include, withoutlimitation, ethynyl (C₂), 1-propynyl (C₃), 2-propynyl (C₃), 1-butynyl(C₄), 2-butynyl (C₄), and the like. Examples of C₂₋₆ alkenyl groupsinclude the aforementioned C₂₋₄ alkynyl groups as well as pentynyl (C₅),hexynyl (C₆), and the like. Additional examples of alkynyl includeheptynyl (C₇), octynyl (C₈), and the like. Unless otherwise specified,each instance of an alkynyl group is independently optionallysubstituted, i.e., unsubstituted (an “unsubstituted alkynyl”) orsubstituted (a “substituted alkynyl”) with one or more substituents. Incertain embodiments, the alkynyl group is unsubstituted C₂₋₁₀ alkynyl.In certain embodiments, the alkynyl group is substituted C₂₋₁₀ alkynyl.

“Carbocyclyl” or “carbocyclic” refers to a radical of a non-aromaticcyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C₃₋₁₀carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. Insome embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms(“C₃₋₈ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, acarbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). Insome embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms(“C₅₋₁₀ carbocyclyl”). Exemplary C₃₋₆ carbocyclyl groups include,without limitation, cyclopropyl (C₃), cyclopropenyl (C₃), cyclobutyl(C₄), cyclobutenyl (C₄), cyclopentyl (C₅), cyclopentenyl (C₅),cyclohexyl (C₆), cyclohexenyl (C₆), cyclohexadienyl (C₆), and the like.Exemplary C₃₋₈ carbocyclyl groups include, without limitation, theaforementioned C₃₋₆ carbocyclyl groups as well as cycloheptyl (C₇),cycloheptenyl (C₇), cycloheptadienyl (C₇), cycloheptatrienyl (C₇),cyclooctyl (C₈), cyclooctenyl (C₈), bicyclo[2.2.1]heptanyl (C₇),bicyclo[2.2.2]octanyl (C₈), and the like. Exemplary C₃₋₁₀ carbocyclylgroups include, without limitation, the aforementioned C₃₋₈ carbocyclylgroups as well as cyclononyl (C₉), cyclononenyl (C₉), cyclodecyl (C₁₀),cyclodecenyl (C₁₀), octahydro-1H-indenyl (C₉), decahydronaphthalenyl(C₁₀), spiro[4.5]decanyl (C₁₀), and the like. As the foregoing examplesillustrate, in certain embodiments, the carbocyclyl group is eithermonocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged orSpiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) andcan be saturated or can be partially unsaturated. “Carbocyclyl” alsoincludes ring systems wherein the carbocyclic ring, as defined above, isfused with one or more aryl or heteroaryl groups wherein the point ofattachment is on the carbocyclic ring, and in such instances, the numberof carbons continue to designate the number of carbons in thecarbocyclic ring system. Unless otherwise each instance of a carbocyclylgroup is independently optionally substituted, i.e., unsubstituted (an“unsubstituted carbocyclyl”) or substituted (a “substitutedcarbocyclyl”) with one or more substituents. In certain embodiments, thecarbocyclyl group is unsubstituted C₃₋₁₀ carbocyclyl. In certainembodiments, the carbocyclyl group is substituted C₃₋₁₀ carbocyclyl.

In some embodiments, “carbocyclyl” is a monocyclic, saturatedcarbocyclyl group having from 3 to 10 ring carbon atoms (“C₃₋₁₀cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ringcarbon atoms (“C₃₋₈ cycloalkyl”). In some embodiments, a cycloalkylgroup has 3 to 6 ring carbon atoms (“C₃₋₆ cycloalkyl”). In someembodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C₅₋₆cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ringcarbon atoms (“C₅₋₁₀ cycloalkyl”). Examples of C₅₋₆ cycloalkyl groupsinclude cyclopentyl (C₅) and cyclohexyl (C₅). Examples of C₃₋₆cycloalkyl groups include the aforementioned C₅₋₆ cycloalkyl groups aswell as cyclopropyl (C₃) and cyclobutyl (C₄). Examples of C₃₋₈cycloalkyl groups include the aforementioned C₃₋₆ cycloalkyl groups aswell as cycloheptyl (C₇) and cyclooctyl (C₈). Unless otherwisespecified, each instance of a cycloalkyl group is independentlyunsubstituted (an “unsubstituted cycloalkyl”) or substituted (a“substituted cycloalkyl”) with one or more substituents. In certainembodiments, the cycloalkyl group is unsubstituted C₃₋₁₀ cycloalkyl. Incertain embodiments, the cycloalkyl group is substituted C₃₋₁₀cycloalkyl.

“Heterocyclyl” or “heterocyclic” refers to a radical of a 3- to10-membered non-aromatic ring system having ring carbon atoms and 1 to 4ring heteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 memberedheterocyclyl”). In heterocyclyl groups that contain one or more nitrogenatoms, the point of attachment can be a carbon or nitrogen atom, asvalency permits. A heterocyclyl group can either be monocyclic(“monocyclic heterocyclyl”) or a fused, bridged, or Spiro ring system,such as a bicyclic system (“bicyclic heterocyclyl”), and can besaturated or can be partially unsaturated. Heterocyclyl bicyclic ringsystems can include one or more heteroatoms in one or both rings.“Heterocyclyl” also includes ring systems wherein the heterocyclic ring,as defined above, is fused with one or more carbocyclyl groups whereinthe point of attachment is either on the carbocyclyl or heterocyclicring, or ring systems wherein the heterocyclic ring, as defined above,is fused with one or more aryl or heteroaryl groups, wherein the pointof attachment is on the heterocyclic ring, and in such instances, thenumber of ring members continue to designate the number of ring membersin the heterocyclic ring system. Unless otherwise specified, eachinstance of heterocyclyl is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a“substituted heterocyclyl”) with one or more substituents. In certainembodiments, the heterocyclyl group is unsubstituted 3-10 memberedheterocyclyl. In certain embodiments, the heterocyclyl group issubstituted 3-10 membered heterocyclyl.

In some embodiments, a heterocyclyl group is a 5-10 membered,non-aromatic ring system having ring carbon atoms and 1-4 ringheteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“5-10 memberedheterocyclyl”). In some embodiments, a heterocyclyl group is a 5-8membered non-aromatic ring system having ring carbon atoms and 1-4 ringheteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, and sulfur (“5-8 membered heterocyclyl”). In someembodiments, a heterocyclyl group is a 5-6 membered non-aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms, wherein eachheteroatom is independently selected from nitrogen, oxygen, and sulfur(“5-6 membered heterocyclyl”). In some embodiments, the 5-6 memberedheterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen,and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2ring heteroatoms selected from nitrogen, oxygen, and sulfur. In someembodiments, the 5-6 membered heterocyclyl has one ring heteroatomselected from nitrogen, oxygen, and sulfur.

Exemplary 3-membered heterocyclyl groups containing one heteroatominclude, without limitation, azirdinyl, oxiranyl, thiiranyl. Exemplary4-membered heterocyclyl groups containing one heteroatom include,without limitation, azetidinyl, oxetanyl and thietanyl. Exemplary5-membered heterocyclyl groups containing one heteroatom include,without limitation, tetrahydropyranyl, dihydrofuranyl,tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl,and pyrrolyl-2,5-dione. Exemplary 5-membered heterocyclyl groupscontaining two heteroatoms include, without limitation, dioxolanyl,oxasulfuranyl, disulfuranyl, and oxazolidin-2-one. Exemplary 5-memberedheterocyclyl groups containing three heteroatoms include, withoutlimitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary6-membered heterocyclyl groups containing one heteroatom include,without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl,and thianyl. Exemplary 6-membered heterocyclyl groups containing twoheteroatoms include, without limitation, piperazinyl, morpholinyl,dithianyl, and dioxanyl. Exemplary 6-membered heterocyclyl groupscontaining two heteroatoms include, without limitation, triazinanyl.Exemplary 7-membered heterocyclyl groups containing one heteroatominclude, without limitation, azepanyl, oxepanyl and thicpanyl. Exemplary8-membered heterocyclyl groups containing one heteroatom include,without limitation, azocanyl, oxetanyl and thiocanyl. Exemplary5-membered heterocyclyl groups fused to a C₆ aryl ring (also referred toherein as a 5,6-bicyclic heterocyclic ring) include, without limitation,indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl,benzoxazolinonyl, and the like. Exemplary 6-membered heterocyclyl groupsfused to an aryl ring (also referred to herein as a 6,6-bicyclicheterocyclic ring) include, without limitation, tetrahydroquinolinyl,tetrahydroisoquinolinyl, and the like.

“Aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclicor tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 pielectrons shared in a cyclic array) having 6-14 ring carbon atoms andzero heteroatoms provided in the aromatic ring system (“C₆₋₁₄ aryl”). Insome embodiments, an aryl group has six ring carbon atoms (“C₆ aryl”;e.g., phenyl). In some embodiments, an aryl group has ten ring carbonatoms (“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). Insome embodiments, an aryl group has fourteen ring carbon atoms (“C₁₄aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein thearyl ring, as defined above, is fused with one or more carbocyclyl orheterocyclyl groups, wherein the radical or point of attachment is onthe aryl ring, and in such instances, the number of carbon atomscontinue to designate the number of carbon atoms in the aryl ringsystem. Unless otherwise specified, each instance of an aryl group isindependently optionally substituted, i.e., unsubstituted (an“unsubstituted aryl”) or substituted (a “substituted aryl”) with one ormore substituents. In certain embodiments, the aryl group isunsubstituted C₆₋₁₄ aryl. In certain embodiments, the aryl group issubstituted C₆₋₁₄ aryl.

“Aralkyl” refers to an optionally substituted alkyl group substituted byan optionally substituted aryl group. In certain embodiments, thearalkyl is optionally substituted benzyl. In certain embodiments, thearalkyl is benzyl. In certain embodiments, the aralkyl is optionallysubstituted phenethyl. In certain embodiments, the aralkyl is phenethyl.

“Heteroaryl” refers to a radical of a 5-10 membered, monocyclic orbicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 pi electronsshared in a cyclic array) having ring carbon atoms and 1-4 ringheteroatoms provided in the aromatic ring system, wherein eachheteroatom is independently selected from nitrogen, oxygen and sulfur(“5-10 membered heteroaryl”). In heteroaryl groups that contain one ormore nitrogen atoms, the point of attachment can be a carbon or nitrogenatom, as valency permits. Heteroaryl bicyclic ring systems can includeone or more heteroatoms in one or both rings. “Heteroaryl” includes ringsystems wherein the heteroaryl ring, as defined above, is fused with oneor more carbocyclyl or heterocyclyl groups wherein the point ofattachment is on the heteroaryl ring, and in such instances, the numberof ring members continue to designate the number of ring members in theheteroaryl ring system. “Heteroaryl” also includes ring systems whereinthe heteroaryl ring, as defined above, is fused with one or more arylgroups wherein the point of attachment is either on the aryl orheteroaryl ring, and in such instances, the number of ring membersdesignates the number of ring members in the fused (aryl/heteroaryl)ring system. Bicyclic heteroaryl groups wherein one ring does notcontain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and thelike) the point of attachment can be on either ring, i.e., either thering bearing a heteroatom (e.g., 2-indolyl) or the ring that does notcontain a heteroatom (e.g., 5-indolyl).

In some embodiments, a heteroaryl group is a 5-10 membered aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-8 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-6 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In someembodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatomsselected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen,oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unlessotherwise specified, each instance of a heteroaryl group isindependently optionally substituted, i.e., unsubstituted (an“unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”)with one or more substituents. In certain embodiments, the heteroarylgroup is unsubstituted 5-14 membered heteroaryl. In certain embodiments,the heteroaryl group is substituted 5-14 membered heteroaryl.

Exemplary 5-membered heteroaryl groups containing one heteroatominclude, without limitation, pyrrolyl, furanyl, and thiophenyl.Exemplary 5-membered heteroaryl groups containing two heteroatomsinclude, without limitation, imidazolyl, pyrazolyl, oxazolyl,isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroarylgroups containing three heteroatoms include, without limitation,triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-memberedheteroaryl groups containing four heteroatoms include, withoutlimitation, tetrazolyl. Exemplary 6-membered heteroaryl groupscontaining one heteroatom include, without limitation, pyridinyl.Exemplary 6-membered heteroaryl groups containing two heteroatomsinclude, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.Exemplary 6-membered heteroaryl groups containing three or fourheteroatoms include, without limitation, triazinyl and tetrazinyl,respectively. Exemplary 7-membered heteroaryl groups containing oneheteroatom include, without limitation, azepinyl, oxepinyl, andthiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, withoutlimitation, indolyl, isoindolyl, indazolyl, benzotriazolyl,benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl,benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl,benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, andpurinyl. Exemplary 6,6-bicyclic heteroaryl groups include, withoutlimitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl,cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.

“Heteroaralkyl” is a subset of alkyl and heteroaryl and refers to anoptionally substituted alkyl group substituted by an optionallysubstituted heteroaryl group.

“Unsaturated” or “partially unsaturated” refers to a group that includesat least one double or triple bond. A “partially unsaturated” ringsystem is further intended to encompass rings having multiple sites ofunsaturation, but is not intended to include aromatic groups (e.g., arylor heteroaryl groups). Likewise, “saturated” refers to a group that doesnot contain a double or triple bond, i.e., contains all single bonds.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylgroups, which are divalent linking groups, are further referred to usingthe suffix -ene, e.g., alkylene, alkenylene, alkynylene, carbocyclylene,heterocyclylene, arylene, and heteroarylene.

An atom, moiety, or group described herein may be unsubstituted orsubstituted, as valency permits, unless otherwise provided expressly.The term “optionally substituted” refers to substituted orunsubstituted.

A group is optionally substituted unless expressly provided otherwise.The term “optionally substituted” refers to being substituted orunsubstituted. In certain embodiments, alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl groups are optionallysubstituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted”or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl,“substituted” or “unsubstituted” carbocyclyl, “substituted” or“unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or“substituted” or “unsubstituted” heteroaryl group). In general, the term“substituted”, whether preceded by the term “optionally” or not, meansthat at least one hydrogen present on a group (e.g., a carbon ornitrogen atom) is replaced with a permissible substituent, e.g., asubstituent which upon substitution results in a stable compound, e.g.,a compound which does not spontaneously undergo transformation such asby rearrangement, cyclization, elimination, or other reaction. Unlessotherwise indicated, a “substituted” group has a substituent at one ormore substitutable positions of the group, and when more than oneposition in any given structure is substituted, the substituent iseither the same or different at each position. The term “substituted” iscontemplated to include substitution with all permissible substituentsof organic compounds, any of the substituents described herein thatresults in the formation of a stable compound. The present disclosurecontemplates any and all such combinations in order to arrive at astable compound. For purposes of this disclosure, heteroatoms such asnitrogen may have hydrogen substituents and/or any suitable substituentas described herein which satisfy the valencies of the heteroatoms andresults in the formation of a stable moiety. In certain embodiments, thesubstituent is a carbon atom substituent. In certain embodiments, thesubstituent is a nitrogen atom substituent. In certain embodiments, thesubstituent is an oxygen atom substituent. In certain embodiments, thesubstituent is a sulfur atom substituent.

Exemplary carbon atom substituents include, but are not limited to,halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(aa), —ON(R^(bb))₂,—N(R^(bb))₂, —N(R^(bb))₃ ⁺X⁻, —N(OR^(cc))R^(bb), —SH, —SR^(aa),—SSR^(cc), —C(═O)R^(aa), —CO₂H, —CHO, —C(OR^(cc))₂, —CO₂R^(aa),—OC(═O)R^(aa), —OCO₂R^(aa), —C(═O)N(R^(bb))₂, —OC(═O)N(R^(bb))₂,—NR^(bb)C(═O)R^(aa), —NR^(bb)CO₂R^(aa), —NR^(bb)C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —OC(═NR^(bb))R^(aa),—OC(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —OC(═NR^(bb))N(R^(bb))₂,—NR^(bb)C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa),—NR^(bb)SO₂R^(aa), —SO₂N(R^(bb))₂, —SO₂R^(aa), —SO₂OR^(aa), —OSO₂R^(aa),—S(═O)R^(aa), —OS(═O)R^(aa), —Si(R^(aa))₃, —OSi(R^(aa))₃—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), —C(═S)SR^(aa), —SC(═S)SR^(aa),—SC(═O)SR^(aa), —OC(═O)SR^(aa), —SC(═O)OR^(aa), —SC(═O)R^(aa),—P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂,—P(═O)(N(R^(bb))₂)₂, —OP(═O)(N(R^(bb))₂)₂, —NR^(bb)P(═O)(R^(aa))₂,—NR^(bb)P(═O)(OR^(cc))₂, —NR^(bb)P(═O)(N(R^(bb))₂)₂, —P(R^(cc))₂,—P(OR^(cc))₂, —P(R^(cc))₃ ⁺X⁻, —P(OR^(cc))₃ ⁺X⁻, —P(R^(cc))₄,—P(OR^(cc))₄, —OP(R^(cc))₂, —OP(R^(cc))₃ ⁺X⁻, —OP(OR^(cc))₂,—OP(OR^(cc))₃ ⁺X⁻, —OP(R^(cc))₄, —OP(OR^(cc))₄, —B(R^(aa))₂,—B(OR^(cc))₂, —BR^(aa)(OR^(cc)), C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl,C₆₋₁₄ aryl, and 5-14 membered heteroaryl, wherein each alkyl, alkenyl,alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;wherein X⁻ is a counterion;

or two geminal hydrogens on a carbon atom are replaced with the group═O, ═S, ═NN(R^(bb))₂, ═NNR^(bb)C(═O)R^(aa), ═NNR^(bb)C(═O)OR^(aa),═NNR^(bb)S(═O)₂R^(aa), ═NR^(bb), or ═NOR^(cc);

each instance of R^(aa) is, independently, selected from C₁₋₁₀ alkyl,C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl,3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, ortwo R^(aa) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(bb) is, independently, selected from hydrogen, —OH,—OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂,—SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc),—C(═S)SR^(cc), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)(N(R^(cc))₂)₂,C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(bb) groups are joined to form a 3-14 memberedheterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl,alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;wherein X⁻ is a counterion;

each instance of R^(cc) is, independently, selected from hydrogen, C₁₋₁₀alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(cc) groups are joined to form a 3-14 memberedheterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl,alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(dd) is, independently, selected from halogen, —CN,—NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(ee), —ON(R^(ff))₂, —N(R^(ff))₂,—N(R^(ff))₃ ⁺X⁻, —N(OR^(ee))R^(ff), —SH, —SR^(ee), —SSR^(ee),—C(═O)R^(ee), —CO₂H, —CO₂R^(ee), —OC(═O)R^(ee), —OCO₂R^(ee),—C(═O)N(R^(ff))₂, —OC(═O)N(R^(ff))₂, —NRC(═O)R^(ee), —NR^(ff)CO₂R^(ee),—NR^(ff)C(═O)N(R^(ff))₂, —C(═NR^(ff))OR^(ee), —OC(═NR^(ff))R^(ee),OC(═NR^(ff))OR^(ee), —C(═NR^(ff))N(R^(ff))₂, —OC(═NR^(ff))N(R^(ff))₂,—NR^(ff)C(═NR^(ff))N(R^(ff))₂, —NR^(ff)SO₂R^(ee), —SO₂N(R^(ff))₂,—SO₂R^(ee), —SO₂OR^(ee), —OSO₂R^(ee), —S(═O)R^(ee), —Si(R^(ee))₃,—OSi(R^(ee))₃, —C(═S)N(R^(ff))₂, —C(═O)SR^(ee), —C(═S)SR^(ee),—SC(═S)SR^(ee), —P(═O)(OR^(ee))₂, —P(═O)(R^(ee))₂, —OP(═O)(R^(ee))₂,—OP(═O)(OR^(ee))₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆alkynyl, C₃₋₁₀ carbocyclyl, 3-10 membered heterocyclyl, C₆₋₁₀ aryl, 5-10membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl,heterocyclyl, aryl, and heteroaryl is independently substituted with 0,1, 2, 3, 4, or 5 R^(gg) groups, or two geminal R^(dd) substituents canbe joined to form ═O or ═S; wherein X⁻ is a counterion;

each instance of R^(ee) is, independently, selected from C₁₋₆ alkyl,C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, whereineach alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, andheteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg)groups;

each instance of R^(ff) is, independently, selected from hydrogen, C₁₋₆alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl,3-10 membered heterocyclyl, C₆₋₁₀ aryl and 5-10 membered heteroaryl, ortwo R^(ff) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups; and

each instance of R^(gg) is, independently, halogen, —CN, —NO₂, —N₃,—SO₂H, —SO₃H, —OH, —OC₁₋₆ alkyl, —ON(C₁₋₆ alkyl)₂, —N(C₁₋₆ alkyl)₂,—N(C₁₋₆ alkyl)₃ ⁺X⁻, —NH(C₁₋₆ alkyl)₂ ⁺X⁻, —NH₂(C₁₋₆ alkyl)⁺X⁻, —NH₃⁺X⁻, —N(OC₁₋₆ alkyl)(C₁₋₆ alkyl), —N(OH)(C₁₋₆ alkyl), —NH(OH), —SC₁₋₆alkyl, —SS(C₁₋₆ alkyl), —C(═O)(C₁₋₆ alkyl), —CO₂H, —CO₂(C₁₋₆ alkyl),—OC(═O)(C₁₋₆ alkyl), —OCO₂(C₁₋₆ alkyl), —C(═O)NH₂, —C(═O)N(C₁₋₆ alkyl)₂,—OC(═O)NH(C₁₋₆ alkyl), —NHC(═O)(C₁₋₆ alkyl), —N(C₁₋₆ alkyl)C(═O)(C₁₋₆alkyl), —NHCO₂(C₁₋₆ alkyl), —NHC(═O)N(C₁₋₆ alkyl)₂, —NHC(═O)NH(C₁₋₆alkyl), —NHC(═O)NH₂, —C(═NH)O(C₁₋₆ alkyl), —OC(═NH)(C₁₋₆ alkyl),—OC(═NH)OC₁₋₆ alkyl, —C(═NH)N(C₁₋₆ alkyl)₂, —C(═NH)NH(C₁₋₆ alkyl),—C(═NH)NH₂, —OC(═NH)N(C₁₋₆ alkyl)₂, —OC(NH)NH(C₁₋₆ alkyl), —OC(NH)NH₂,—NHC(NH)N(C₁₋₆ alkyl)₂, —NHC(═NH)NH₂, —NHSO₂(C₁₋₆ alkyl), —SO₂N(C₁₋₆alkyl)₂, —SO₂NH(C₁₋₆ alkyl), —SO₂NH₂, —SO₂C₁₋₆ alkyl, —SO₂OC₁₋₆ alkyl,—OSO₂C₁₋₆ alkyl, —SOC₁₋₆ —Si(C₁₋₆ alkyl)₃, —OSi(C₁₋₆ alkyl)₃—C(═S)N(C₁₋₆ alkyl)₂, C(═S)NH(C₁₋₆ alkyl), C(═S)NH₂, —C(═O)S(C₁₋₆alkyl), —C(═S)SC₁₋₆ alkyl, —SC(═S)SC₁₋₆ alkyl, —P(═O)₂(C₁₋₆ alkyl),—P(═O)(C₁₋₆ alkyl)₂, —OP(═O)(C₁₋₆ alkyl)₂, —OP(═O)(OC₁₋₆ alkyl)₂, C₁₋₆alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl,C₆₋₁₀ aryl, 3-10 membered heterocyclyl, 5-10 membered heteroaryl; or twogeminal R^(gg) substituents can be joined to form ═O or ═S; wherein X⁻is a counterion.

A “counterion” or “anionic counterion” is a negatively charged groupassociated with a cationic quaternary amino group in order to maintainelectronic neutrality. An anionic counterion may be monovalent (i.e.,including one formal negative charge). An anionic counterion may also bemultivalent (i.e., including more than one formal negative charge), suchas divalent or trivalent. Exemplary counterions include halide ions(e.g., F⁻, Cl⁻, Br⁻, I⁻), NO₃ ⁻, ClO₄ ⁻, OH⁻, H₂PO₄ ⁻, HCO₃ ⁻, HSO₄ ⁻,sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate,p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate,naphthalene-2-sulfonate, naphthalene-1-sulfonic acid-5-sulfonate,ethan-1-sulfonic acid-2-sulfonate, and the like), carboxylate ions(e.g., acetate, propanoate, benzoate, glycerate, lactate, tartrate,glycolate, gluconate, and the like), BF₄ ⁻, PF₄ ⁻, PF₆ ⁻, AsF₆ ⁻, SbF₆⁻, B[3,5-(CF₃)₂C₆H₃]₄]⁻, B(C₆F₅)₄ ⁻, BPh₄ ⁻, Al(OC(CF₃)₃)₄ ⁻, andcarborane anions (e.g., CB₁₁H₁₂ ⁻ or (HCB₁₁Me₅Br₆)⁻). Exemplarycounterions which may be multivalent include CO₃ ²⁻, HPO₄ ²⁻, PO₄ ³⁻,B₄O₇ ²⁻, SO₄ ²⁻, S₂O₃ ²⁻, carboxylate anions (e.g., tartrate, citrate,fumarate, maleate, malate, malonate, gluconate, succinate, glutarate,adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates,aspartate, glutamate, and the like), and carboranes.

“Halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro,—Cl), bromine (bromo, —Br), or iodine (iodo, —I).

“Acyl” refers to a moiety selected from the group consisting of—C(═O)R^(aa), —CHO, —CO₂R^(aa), —C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa),—C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa),—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), or —C(═S)SR^(aa), wherein R^(aa) andR^(bb) are as defined herein.

Nitrogen atoms can be substituted or unsubstituted as valency permits,and include primary, secondary, tertiary, and quaternary nitrogen atoms.Exemplary nitrogen atom substituents include, but are not limited to,hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa),—C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(bb))R^(aa),—C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc),—SO₂OR^(cc), —SOR^(aa)a, —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc),—P(═O) (OR^(cc))₂, —P(═O)(R^(aa))₂, —P(═O)(N(R^(cc))₂)₂, C₁₋₁₀ alkyl,C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl,3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, ortwo R^(cc) groups attached to a nitrogen atom are joined to form a 3-14membered heterocyclyl or 5-14 membered heteroaryl ring, wherein eachalkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylis independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups, andwherein R^(aa), R^(bb), R^(cc), and R^(dd) are as defined above.

In certain embodiments, the substituent present on a nitrogen atom is anitrogen protecting group (also referred to as an amino protectinggroup). Nitrogen protecting groups include, but are not limited to, —OH,—OR^(aa), —N(R^(cc))₂, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))R^(aa), —C(═NR^(cc))OR^(aa),—C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc),—SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), C₁₋₁₀ alkyl(e.g., aralkyl, heteroaralkyl), C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl,heterocyclyl, aralkyl, aryl, and heteroaryl is independently substitutedwith 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb),R^(cc) and R^(dd) are as defined herein. Nitrogen protecting groups arewell known in the art and include those described in detail inProtecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts,3^(rd) edition, John Wiley & Sons, 1999, incorporated herein byreference.

For example, nitrogen protecting groups such as amide groups (e.g.,—C(═O)R^(aa)) include, but are not limited to, formamide, acetamide,chloroacetamide, trichloroacetamide, trifluoroacetamide,phenylacetamide, 3-phenylpropanamide, picolinamide,3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide,p-phenylbenzamide, o-nitrophenylacetamide, o-nitrophenoxyacetamide,acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide,3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide,2-methyl-2-(o-nitrophenoxy)propanamide,2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide,3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethioninederivative, o-nitrobenzamide, and o-(benzoyloxymethyl)benzamide.

Nitrogen protecting groups such as carbamate groups (e.g.,—C(═O)OR^(aa)) include, but are not limited to, methyl carbamate, ethylcarbamate, 9-fluorenylmethyl carbamate (Fmoc),9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluorenylmethylcarbamate,2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methylcarbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc),2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate(Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethylcarbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate,1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC),1,1-dimethyl-2,2,2-trichloroethyl carbamate1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc),1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethylcarbamate, t-butyl carbamate (BOC or Boc), 1-adamantyl carbamate (Adoc),vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropylallylcarbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate(Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithiocarbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz),p-nitobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzylcarbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzylcarbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate,2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate,2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methylcarbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc),2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate(Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc),1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate,p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate,2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenylcarbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate,3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methylcarbamate, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzylcarbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentylcarbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate,2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzylcarbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate,1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate,2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate,isobutyl carbamate, isonicotinyl carbamate,p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate,1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate,1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate,1-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethylcarbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate,p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate,4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzylcarbamate.

Nitrogen protecting groups such as sulfonamide groups (e.g.,—S(═O)₂R^(aa)) include, but are not limited to, p-toluenesulfonamide(Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide(Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb),2,6-dimethyl-4-methoxybenzenesulfonamide (Pme),2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte),4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide(Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds),2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide(Ms), β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide,4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS),benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.

Other nitrogen protecting groups include, but are not limited to,phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacylderivative, N′-phenylaminothioacyl N-benzoylphenylalanyl derivative,N-acetylmethionine derivative, 4,5-diphenyl-3-oxazolin-2-one,N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide,N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentaneadduct (STABASE), 5-substituted1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted3,5-dinitro-4-pyridone, N-methylamine, N-allylamine,N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine,N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammoniumsalts, N-benzylamine, N-di(4-methoxyphenyl)methylamine,N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr),N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr),N-9-phenylfluorenylamine (PhF),N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm),N-2-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine,N-benzylideneamine, N-p-methoxybenzylideneamine,N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine,N—(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine,N-p-nitrobenzylideneamine, N-salicylideneamine,N-5-chlorosalicylideneamine,N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine,N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine,N-borane derivative, N-diphenylborinic acid derivative,N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper chelate,N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide,diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt),diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzylphosphoramidate, diphenyl phosphoramidate, benzenesulfenamide,o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide,pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide,triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys).

Exemplary oxygen atom substituents include, but are not limited to,—R^(aa), —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃ ⁺X⁻,—P(OR^(cc))₂, —P(OR^(cc))₃ ⁺X⁻, —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, and—P(═O)(N(R^(bb))₂)₂, wherein X⁻, R^(aa), R^(bb), and R^(cc) are asdefined herein. In certain embodiments, the oxygen atom substituentpresent on an oxygen atom is an oxygen protecting group (also referredto as a hydroxyl protecting group). Oxygen protecting groups are wellknown in the art and include those described in detail in ProtectingGroups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd)edition, John Wiley & Sons, 1999, incorporated herein by reference.Exemplary oxygen protecting groups include, but are not limited to,methyl, t-butyloxycarbonyl (BOC or Boc), methoxylmethyl (MOM),methylthiomethyl (MTM), t-butylthiomethyl,(phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM),p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM),guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM),siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl,bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyltetrahydropyranyl (THP), 3-bromotetrahydropyranyl,tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl(MTHP), 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranylS,S-dioxide, 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl(CTMP), 1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl,2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl,1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl,1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl,2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl,t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl,benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl,p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl,p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido,diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl,triphenylmethyl, a-naphthyldiphenylmethyl,p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl,tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl,4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl,4,4′,4″-tris(levulinoyloxyphenyl)methyl,4,4′,4″-tris(benzoyloxyphenyl)methyl,3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl,1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl,9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl,1,3-benzodisulfuran-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl(TMS), triethylsilyl (TES), triisopropylsilyl (TIPS),dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS),dimethylthexylsilyl, t-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl(TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl,diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate,benzoylformate, acetate, chloroacetate, dichloroacetate,trichloroacetate, trifluoroacetate, methoxyacetate,triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate,3-phenylpropionate, 4-oxopentanoate (levulinate),4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate,adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate,2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate,9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate(TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec),2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutylcarbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkylp-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzylcarbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o-nitrobenzylcarbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate,4-ethoxy-1-napththyl carbonate, methyl dithiocarbonate, 2-iodobenzoate,4-azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate,2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl,4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate,2,6-dichloro-4-methylphenoxyacetate,2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate,2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate,isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate,o-(methoxyacyl)benzoate, α-naphthoate, nitrate, alkylN,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate,borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate,sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate(Ts).

Exemplary sulfur atom substituents include, but are not limited to,—R^(aa), —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃ ⁺X⁻,—P(OR^(cc))₂, —P(OR^(cc))₃ ⁺X⁻, —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, and—P(═O)(N(R^(bb))₂)₂, wherein R^(aa), R^(bb), and R^(cc) are as definedherein. In certain embodiments, the sulfur atom substituent present on asulfur atom is a sulfur protecting group (also referred to as a thiolprotecting group). Sulfur protecting groups are well known in the artand include those described in detail in Protecting Groups in OrganicSynthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley &Sons, 1999, incorporated herein by reference.

A “hydrocarbon chain” refers to a substituted or unsubstituted divalentalkyl, alkenyl, or alkynyl group. A hydrocarbon chain includes (1) oneor more chains of carbon atoms immediately between the two radicals ofthe hydrocarbon chain; (2) optionally one or more hydrogen atoms on thechain(s) of carbon atoms; and (3) optionally one or more substituents(“non-chain substituents,” which are not hydrogen) on the chain(s) ofcarbon atoms. A chain of carbon atoms consists of consecutivelyconnected carbon atoms (“chain atoms” or “carbon units”) and does notinclude hydrogen atoms or heteroatoms. However, a non-chain substituentof a hydrocarbon chain may include any atoms, including hydrogen atoms,carbon atoms, and heteroatoms. For example, hydrocarbon chain—C^(A)H(C^(B)H₂C^(C)H₃)— includes one chain atom C^(A), one hydrogenatom on C^(A), and non-chain substituent —(C^(B)H₂C^(C)H₃). The term“C_(x) hydrocarbon chain,” wherein x is a positive integer, refers to ahydrocarbon chain that includes x number of chain atom(s) between thetwo radicals of the hydrocarbon chain. If there is more than onepossible value of x, the smallest possible value of x is used for thedefinition of the hydrocarbon chain. For example, —CH(C₂H₅)— is a C₁hydrocarbon chain, and

is a C₃ hydrocarbon chain. When a range of values is used, the meaningof the range is as described herein. For example, a C₃₋₁₀ hydrocarbonchain refers to a hydrocarbon chain where the number of chain atoms ofthe shortest chain of carbon atoms immediately between the two radicalsof the hydrocarbon chain is 3, 4, 5, 6, 7, 8, 9, or 10. A hydrocarbonchain may be saturated (e.g., —(CH₂)₄—). A hydrocarbon chain may also beunsaturated and include one or more C═C and/or C≡C bonds anywhere in thehydrocarbon chain. For instance, —CH═CH—(CH₂)₂—, —CH₂—C≡C—CH₂—, and—C≡C—CH═CH— are all examples of a unsubstituted and unsaturatedhydrocarbon chain. In certain embodiments, the hydrocarbon chain isunsubstituted (e.g., —C≡C— or —(CH₂)₄—). In certain embodiments, thehydrocarbon chain is substituted (e.g., —CH(C₂H₅)— and —CF₂—). Any twosubstituents on the hydrocarbon chain may be joined to form anoptionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, or optionally substituted heteroaryl ring.For instance,

are all examples of a hydrocarbon chain. In contrast, in certainembodiments,

are not within the scope of the hydrocarbon chains described herein.When a chain atom of a C_(x) hydrocarbon chain is replaced with aheteroatom, the resulting group is referred to as a C_(x) hydrocarbonchain wherein a chain atom is replaced with a heteroatom, as opposed toa C_(x-1) hydrocarbon chain. For example,

is a C₃ hydrocarbon chain wherein one chain atom is replaced with anoxygen atom.

The term “leaving group” is given its ordinary meaning in the art ofsynthetic organic chemistry and refers to an atom or a group capable ofbeing displaced by a nucleophile. See, for example, Smith, MarchAdvanced Organic Chemistry 6th ed. (501-502). Examples of suitableleaving groups include, but are not limited to, halogen (such as F, Cl,Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy,alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy),arylcarbonyloxy, aryloxy, methoxy, N,O-dimethylhydroxylamino, pixyl, andhaloformates. Exemplary leaving groups include, but are not limited to,activated substituted hydroxyl groups (e.g., —OC(═O)SR^(aa),—OC(═O)R^(aa), —OCO₂R^(aa), —OC(═O)N(R^(bb))₂, —OC(═NR^(bb))R^(aa),—OC(═NR^(bb))OR^(aa), —OC(═NR^(bb))N(R^(bb))₂, —OS(═O)R^(aa),—OSO₂R^(aa), —OP(R^(cc))₂, —OP(R^(cc))₃, —OP(═O)₂R^(aa),—OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂, —OP(═O)₂N(R^(bb))₂, and—OP(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as definedherein). In some cases, the leaving group is a sulfonic acid ester, suchas toluenesulfonate (tosylate, -OTs), methanesulfonate (mesylate, -OMs),p-bromobenzenesulfonyloxy (brosylate, -OBs), —OS(═O)₂(CF₂)₃CF₃(nonaflate, -ONf), or trifluoromethanesulfonate (triflate, -OTf). Insome cases, the leaving group is a brosylate, such asp-bromobenzenesulfonyloxy. In some cases, the leaving group is anosylate, such as 2-nitrobenzenesulfonyloxy. The leaving group may alsobe a phosphineoxide (e.g., formed during a Mitsunobu reaction) or aninternal leaving group such as an epoxide or cyclic sulfate. Othernon-limiting examples of leaving groups are water, ammonia, alcohols,ether moieties, thioether moieties, zinc halides, magnesium moieties,diazonium salts, and copper moieties.

Other Definitions

The term “pharmaceutically acceptable salt” refers to those salts whichare, within the scope of sound medical judgment, suitable for use incontact with the tissues of humans and lower animals without unduetoxicity, irritation, allergic response, and the like, and arecommensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts are well known in the art. For example, Berge et al.describe pharmaceutically acceptable salts in detail in J.Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein byreference. Pharmaceutically acceptable salts of the compounds describedherein include those derived from suitable inorganic and organic acidsand bases. Examples of pharmaceutically acceptable, nontoxic acidaddition salts are salts of an amino group formed with inorganic acidssuch as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuricacid, and perchloric acid or with organic acids such as acetic acid,oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, ormalonic acid or by using other methods known in the art such as ionexchange. Other pharmaceutically acceptable salts include adipate,alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate,borate, butyrate, camphorate, camphorsulfonate, citrate,cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate,formate, fumarate, glucoheptonate, glycerophosphate, gluconate,hemisulfate, heptanoate, hexanoate, hydroiodide,2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, laurylsulfate, malate, maleate, malonate, methanesulfonate,2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate,pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate,pivalate, propionate, stearate, succinate, sulfate, tartrate,thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and thelike. Salts derived from appropriate bases include alkali metal,alkaline earth metal, ammonium and N⁺(C₁₋₄ alkyl)₄ ⁻ salts.Representative alkali or alkaline earth metal salts include sodium,lithium, potassium, calcium, magnesium, and the like. Furtherpharmaceutically acceptable salts include, when appropriate, nontoxicammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carboxylate, sulfate, phosphate,nitrate, lower alkyl sulfonate, and aryl sulfonate.

The term “solvate” refers to forms of the compound that are associatedwith a solvent, usually by a solvolysis reaction. This physicalassociation may include hydrogen bonding. Conventional solvents includewater, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and thelike. The compounds described herein may be prepared, e.g., incrystalline form, and may be solvated. Suitable solvates includepharmaceutically acceptable solvates and further include bothstoichiometric solvates and non-stoichiometric solvates. In certaininstances, the solvate will be capable of isolation, for example, whenone or more solvent molecules are incorporated in the crystal lattice ofa crystalline solid. “Solvate” encompasses both solution-phase andisolatable solvates. Representative solvates include hydrates,ethanolates, and methanolates.

The term “hydrate” refers to a compound that is associated with water.Typically, the number of the water molecules contained in a hydrate of acompound is in a definite ratio to the number of the compound moleculesin the hydrate. Therefore, a hydrate of a compound may be represented,for example, by the general formula R.x H₂O, wherein R is the compound,and x is a number greater than 0. A given compound may form more thanone type of hydrate, including, e.g., monohydrates (x is 1), lowerhydrates (x is a number greater than 0 and smaller than 1, e.g.,hemihydrates (R.0.5 H₂O)), and polyhydrates (x is a number greater than1, e.g., dihydrates (R.2H₂O) and hexahydrates (R.6H₂O)).

The term “tautomers” or “tautomeric” refers to two or moreinterconvertible compounds resulting from at least one formal migrationof a hydrogen atom and at least one change in valency (e.g., a singlebond to a double bond, a triple bond to a single bond, or vice versa).The exact ratio of the tautomers depends on several factors, includingtemperature, solvent, and pH. Tautomerizations (i.e., the reactionproviding a tautomeric pair) may catalyzed by acid or base. Exemplarytautomerizations include keto-to-enol, amide-to-imide, lactam-to-lactim,enamine-to-imine, and enamine-to-(a different enamine) tautomerizations.

It is also to be understood that compounds that have the same molecularformula but differ in the nature or sequence of bonding of their atomsor the arrangement of their atoms in space are termed “isomers”. Isomersthat differ in the arrangement of their atoms in space are termed“stereoisomers”.

Stereoisomers that are not mirror images of one another are termed“diastereomers” and those that are non-superimposable mirror images ofeach other are termed “enantiomers”. When a compound has an asymmetriccenter, for example, it is bonded to four different groups, a pair ofenantiomers is possible. An enantiomer can be characterized by theabsolute configuration of its asymmetric center and is described by theR- and S-sequencing rules of Cahn and Prelog, or by the manner in whichthe molecule rotates the plane of polarized light and designated asdextrorotatory or levorotatory (i.e., as (+) or (−)-isomersrespectively). A chiral compound can exist as either individualenantiomer or as a mixture thereof. A mixture containing equalproportions of the enantiomers is called a “racemic mixture”.

The term “polymorphs” refers to a crystalline form of a compound (or asalt, hydrate, or solvate thereof) in a particular crystal packingarrangement. All polymorphs have the same elemental composition.Different crystalline forms usually have different X-ray diffractionpatterns, infrared spectra, melting points, density, hardness, crystalshape, optical and electrical properties, stability, and solubility.Recrystallization solvent, rate of crystallization, storage temperature,and other factors may cause one crystal form to dominate. Variouspolymorphs of a compound can be prepared by crystallization underdifferent conditions.

The term “co-crystal” refers to a crystalline structure composed of atleast two components. In certain embodiments, a co-crystal may contain acompound of the present invention and one or more other component,including but not limited to, atoms, ions, molecules, or solventmolecules. In certain embodiments, a co-crystal may contain a compoundof the present invention and one or more components related to saidcompound, including not limited to, an isomer, tautomer, salt, solvate,hydrate, synthetic precursor, synthetic derivative, fragment or impurityof said compound.

The term “isotopically labeled derivative” or “isotopically labeled”refers to a compound wherein one or more atoms in the compound (or in anassociated ion or molecule of a salt, hydrate, or solvate) has beenreplaced with an isotope of the same element. For the given element orposition in the molecule the isotope will be enriched, or present in ahigher percentage of all atoms of the element or of all atoms at theposition in the molecule in a sample, relative to an unlabeled variant.In certain embodiments, the enriched isotope will be a stable isotope.In certain embodiments, the enriched isotope will be an unstable orradioactive isotope (e.g., a radionuclide). In certain embodiments, theenriched isotope may be detected by a measurement technique, includingbut not limited to nuclear magnetic resonance, mass spectrometry,infrared spectroscopy, or a technique that measures radioactive decay.

The term “prodrugs” refers to compounds that have cleavable groups andbecome by solvolysis or under physiological conditions the compoundsdescribed herein, which are pharmaceutically active in vivo. Suchexamples include, but are not limited to, choline ester derivatives andthe like, N-alkylmorpholine esters and the like. Other derivatives ofthe compounds described herein have activity in both their acid and acidderivative forms, but in the acid sensitive form often offer advantagesof solubility, tissue compatibility, or delayed release in the mammalianorganism (see, Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24,Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well knownto practitioners of the art, such as, for example, esters prepared byreaction of the parent acid with a suitable alcohol, or amides preparedby reaction of the parent acid compound with a substituted orunsubstituted amine, or acid anhydrides, or mixed anhydrides. Simplealiphatic or aromatic esters, amides, and anhydrides derived from acidicgroups pendant on the compounds described herein are particularprodrugs. In some cases it is desirable to prepare double ester typeprodrugs such as (acyloxy)alkyl esters or((alkoxycarbonyl)oxy)alkylesters. C₁-C₈ alkyl, C₂-C₈ alkenyl, C₂-C₈alkynyl, aryl, C₇-C₁₂ substituted aryl, and C₇-C₁₂ arylalkyl esters ofthe compounds described herein may be preferred.

The term “inhibition”, “inhibiting”, “inhibit,” or “inhibitor” refer tothe ability of a compound to reduce, slow, halt or prevent activity of aparticular biological process (e.g., activity of a bromodomain and/or abromodomain-containing protein) in a cell relative to vehicle.

When a compound, pharmaceutical composition, method, use, or kit isreferred to as “selectively,” “specifically,” or “competitively” bindinga first protein or a first chromatin, the compound, pharmaceuticalcomposition, method, use, or kit binds the first protein or the firstchromatin with a higher binding affinity (e.g., not less than about2-fold, not less than about 5-fold, not less than about 10-fold, notless than about 30-fold, not less than about 100-fold, not less thanabout 1,000-fold, or not less than about 10,000-fold) than binding asecond protein or second chromatin that is different from the firstprotein and the first chromatin. When a compound, pharmaceuticalcomposition, method, use, or kit is referred to as “selectively,”“specifically,” or “competitively” modulating (e.g., increasing orinhibiting) the activity of a bromodomain-containing protein, thecompound, pharmaceutical composition, method, use, or kit modulates theactivity of the bromodomain-containing protein to a greater extent(e.g., not less than about 2-fold, not less than about 5-fold, not lessthan about 10-fold, not less than about 30-fold, not less than about100-fold, not less than about 1,000-fold, or not less than about10,000-fold) than the activity of at least one protein that is differentfrom the bromodomain-containing protein.

The term “aberrant activity” refers to activity deviating from normalactivity, that is, abnormal activity. The term “increased activity”refers to activity higher than normal activity.

The terms “composition” and “formulation” are used interchangeably.

A “subject” to which administration is contemplated refers to a human(i.e., male or female of any age group, e.g., pediatric subject (e.g.,infant, child, or adolescent) or adult subject (e.g., young adult,middle-aged adult, or senior adult)) or non-human animal. In certainembodiments, the non-human animal is a mammal (e.g., primate (e.g.,cynomolgus monkey or rhesus monkey), commercially relevant mammal (e.g.,cattle, pig, horse, sheep, goat, cat, or dog), or bird (e.g.,commercially relevant bird, such as chicken, duck, goose, or turkey)).In certain embodiments, the non-human animal is a fish, reptile, oramphibian. The non-human animal may be a male or female at any stage ofdevelopment. The non-human animal may be a transgenic animal orgenetically engineered animal. A “patient” refers to a human subject inneed of treatment of a disease. The subject may also be a plant. Incertain embodiments, the plant is a land plant. In certain embodiments,the plant is a non-vascular land plant. In certain embodiments, theplant is a vascular land plant. In certain embodiments, the plant is aseed plant. In certain embodiments, the plant is a cultivated plant. Incertain embodiments, the plant is a dicot. In certain embodiments, theplant is a monocot. In certain embodiments, the plant is a floweringplant. In some embodiments, the plant is a cereal plant, e.g., maize,corn, wheat, rice, oat, barley, rye, or millet. In some embodiments, theplant is a legume, e.g., a bean plant, e.g., soybean plant. In someembodiments, the plant is a tree or shrub.

The term “biological sample” refers to any sample including tissuesamples (such as tissue sections and needle biopsies of a tissue); cellsamples (e.g., cytological smears (such as Pap or blood smears) orsamples of cells obtained by microdissection); samples of wholeorganisms (such as samples of yeasts or bacteria); or cell fractions,fragments or organelles (such as obtained by lysing cells and separatingthe components thereof by centrifugation or otherwise). Other examplesof biological samples include blood, serum, urine, semen, fecal matter,cerebrospinal fluid, interstitial fluid, mucous, tears, sweat, pus,biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy),nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccalswabs), or any material containing biomolecules that is derived fromanother biological sample.

The terms “administer,” “administering,” or “administration” refers toimplanting, absorbing, ingesting, injecting, inhaling, or otherwiseintroducing a compound described herein, or a composition thereof, into,in, or on a subject.

The terms “treatment,” “treat,” and “treating” refer to reversing,alleviating, delaying the onset of, or inhibiting the progress of adisease described herein. In some embodiments, treatment may beadministered after one or more signs or symptoms of the disease havedeveloped or have been observed. In other embodiments, treatment may beadministered in the absence of signs or symptoms of the disease. Forexample, treatment may be administered to a susceptible subject prior tothe onset of symptoms (e.g., in light of a history of symptoms and/or inlight of exposure to a pathogen). Treatment may also be continued aftersymptoms have resolved, for example, to delay or prevent recurrence.

The terms “condition,” “disease,” and “disorder” are usedinterchangeably.

An “effective amount” of a compound described herein refers to an amountsufficient to elicit the desired biological response, i.e., treating thecondition. As will be appreciated by those of ordinary skill in thisart, the effective amount of a compound described herein may varydepending on such factors as the desired biological endpoint, thepharmacokinetics of the compound, the condition being treated, the modeof administration, and the age and health of the subject. In certainembodiments, an effective amount is a therapeutically effective amount.In certain embodiments, an effective amount is a prophylactic treatment.In certain embodiments, an effective amount is the amount of a compounddescribed herein in a single dose. In certain embodiments, an effectiveamount is the combined amounts of a compound described herein inmultiple doses.

A “therapeutically effective amount” of a compound described herein isan amount sufficient to provide a therapeutic benefit in the treatmentof a condition or to delay or minimize one or more symptoms associatedwith the condition. A therapeutically effective amount of a compoundmeans an amount of therapeutic agent, alone or in combination with othertherapies, which provides a therapeutic benefit in the treatment of thecondition. The term “therapeutically effective amount” can encompass anamount that improves overall therapy, reduces or avoids symptoms, signs,or causes of the condition, and/or enhances the therapeutic efficacy ofanother therapeutic agent.

A “prophylactically effective amount” of a compound described herein isan amount sufficient to prevent a condition, or one or more symptomsassociated with the condition or prevent its recurrence. Aprophylactically effective amount of a compound means an amount of atherapeutic agent, alone or in combination with other agents, whichprovides a prophylactic benefit in the prevention of the condition. Theterm “prophylactically effective amount” can encompass an amount thatimproves overall prophylaxis or enhances the prophylactic efficacy ofanother prophylactic agent.

A “proliferative disease” refers to a disease that occurs due toabnormal growth or extension by the multiplication of cells (Walker,Cambridge Dictionary of Biology; Cambridge University Press: Cambridge,UK, 1990). A proliferative disease may be associated with: 1) thepathological proliferation of normally quiescent cells; 2) thepathological migration of cells from their normal location (e.g.,metastasis of neoplastic cells); 3) the pathological expression ofproteolytic enzymes such as the matrix metalloproteinases (e.g.,collagenases, gelatinases, and elastases); or 4) the pathologicalangiogenesis as in proliferative retinopathy and tumor metastasis.Exemplary proliferative diseases include cancers (i.e., “malignantneoplasms”), benign neoplasms, diseases associated with angiogenesis,inflammatory diseases, and autoimmune diseases.

The term “angiogenesis” refers to the physiological process throughwhich new blood vessels form from pre-existing vessels. Angiogenesis isdistinct from vasculogenesis, which is the de novo formation ofendothelial cells from mesoderm cell precursors. The first vessels in adeveloping embryo form through vasculogenesis, after which angiogenesisis responsible for most blood vessel growth during normal or abnormaldevelopment. Angiogenesis is a vital process in growth and development,as well as in wound healing and in the formation of granulation tissue.However, angiogenesis is also a fundamental step in the transition oftumors from a benign state to a malignant one, leading to the use ofangiogenesis inhibitors in the treatment of cancer. Angiogenesis may bechemically stimulated by angiogenic proteins, such as growth factors(e.g., VEGF). “Pathological angiogenesis” refers to abnormal (e.g.,excessive or insufficient) angiogenesis that amounts to and/or isassociated with a disease.

The terms “neoplasm” and “tumor” are used herein interchangeably andrefer to an abnormal mass of tissue wherein the growth of the masssurpasses and is not coordinated as in the growth of normal tissue. Aneoplasm or tumor may be “benign” or “malignant,” depending on thefollowing characteristics: degree of cellular differentiation (includingmorphology and functionality), rate of growth, local invasion, andmetastasis. A “benign neoplasm” is generally well differentiated, hascharacteristically slower growth than a malignant neoplasm, and remainslocalized to the site of origin. In addition, a benign neoplasm does nothave the capacity to infiltrate, invade, or metastasize to distantsites. Exemplary benign neoplasms include, but are not limited to,lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheickeratoses, lentigos, and sebaceous hyperplasias. In some cases, certain“benign” tumors may later give rise to malignant neoplasms, which mayresult from additional genetic changes in a subpopulation of the tumor'sneoplastic cells, and these tumors are referred to as “pre-malignantneoplasms.” An exemplary pre-malignant neoplasm is a teratoma. Incontrast, a “malignant neoplasm” is generally poorly differentiated(anaplasia) and has characteristically rapid growth accompanied byprogressive infiltration, invasion, and destruction of the surroundingtissue. Furthermore, a malignant neoplasm generally has the capacity tometastasize to distant sites. The term “metastasis,” “metastatic,” or“metastasize” refers to the spread or migration of cancerous cells froma primary or original tumor to another organ or tissue and is typicallyidentifiable by the presence of a “secondary tumor” or “secondary cellmass” of the tissue type of the primary or original tumor and not ofthat of the organ or tissue in which the secondary (metastatic) tumor islocated. For example, a prostate cancer that has migrated to bone issaid to be metastasized prostate cancer and includes cancerous prostatecancer cells growing in bone tissue.

The term “cancer” refers to a class of diseases characterized by thedevelopment of abnormal cells that proliferate uncontrollably and havethe ability to infiltrate and destroy normal body tissues. See, e.g.,Stedman's Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins:Philadelphia, 1990. Exemplary cancers include, but are not limited to,hematological malignancies. Additional exemplary cancers include, butare not limited to, acoustic neuroma; adenocarcinoma; adrenal glandcancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma,lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benignmonoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma);bladder cancer; breast cancer (e.g., adenocarcinoma of the breast,papillary carcinoma of the breast, mammary cancer, medullary carcinomaof the breast, triple negative breast cancer (TNBC)); brain cancer(e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma,oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor;cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma;chordoma; craniopharyngioma; colorectal cancer (e.g., colon cancer,rectal cancer, colorectal adenocarcinoma); connective tissue cancer;epithelial carcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi'ssarcoma, multiple idiopathic hemorrhagic sarcoma); endometrial cancer(e.g., uterine cancer, uterine sarcoma); esophageal cancer (e.g.,adenocarcinoma of the esophagus, Barrett's adenocarcinoma); Ewing'ssarcoma; ocular cancer (e.g., intraocular melanoma, retinoblastoma);familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g.,stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germcell cancer; head and neck cancer (e.g., head and neck squamous cellcarcinoma, oral cancer (e.g., oral squamous cell carcinoma), throatcancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngealcancer, oropharyngeal cancer)); heavy chain disease (e.g., alpha chaindisease, gamma chain disease, mu chain disease; hemangioblastoma;hypopharynx cancer; inflammatory myofibroblastic tumors; immunocyticamyloidosis; kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor,renal cell carcinoma); liver cancer (e.g., hepatocellular cancer (HCC),malignant hepatoma); lung cancer (e.g., bronchogenic carcinoma, smallcell lung cancer (SCLC), non-small cell lung cancer (NSCLC),adenocarcinoma of the lung); leiomyosarcoma (LMS); mastocytosis (e.g.,systemic mastocytosis); muscle cancer; myelodysplastic syndrome (MDS);mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera(PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM)a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronicmyelocytic leukemia (CML), chronic neutrophilic leukemia (CNL),hypereosinophilic syndrome (HES)); neuroblastoma; neurofibroma (e.g.,neurofibromatosis (NF) type 1 or type 2, schwannomatosis);neuroendocrine cancer (e.g., gastroenteropancreatic neuroendocrine tumor(GEP-NET), carcinoid tumor); osteosarcoma (e.g., bone cancer); ovariancancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarianadenocarcinoma); papillary adenocarcinoma; pancreatic cancer (e.g.,pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm(IPMN), Islet cell tumors); penile cancer (e.g., Paget's disease of thepenis and scrotum); pinealoma; primitive neuroectodermal tumor (PNT);plasma cell neoplasia; paraneoplastic syndromes; intraepithelialneoplasms; prostate cancer (e.g., prostate adenocarcinoma); rectalcancer; rhabdomyosarcoma; salivary gland cancer; skin cancer (e.g.,squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basalcell carcinoma (BCC)); small bowel cancer (e.g., appendix cancer); softtissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma,malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma,fibrosarcoma, myxosarcoma); sebaceous gland carcinoma; small intestinecancer; sweat gland carcinoma; synovioma; testicular cancer (e.g.,seminoma, testicular embryonal carcinoma); thyroid cancer (e.g.,papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC),medullary thyroid cancer); urethral cancer; vaginal cancer; and vulvarcancer (e.g., Paget's disease of the vulva).

The term “hematological malignancy” refers to tumors that affect blood,bone marrow, and/or lymph nodes. Exemplary hematological malignanciesinclude, but are not limited to, leukemia, such as acute lymphoblasticleukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia(AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML)(e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL)(e.g., B-cell CLL, T-cell CLL)); lymphoma, such as Hodgkin lymphoma (HL)(e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g.,B-cell NHL, such as diffuse large cell lymphoma (DLCL) (e.g., diffuselarge B-cell lymphoma (DLBCL, e.g., activated B-cell (ABC) DLBCL(ABC-DLBCL))), follicular lymphoma, chronic lymphocytic leukemia/smalllymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginalzone B-cell lymphoma (e.g., mucosa-associated lymphoid tissue (MALT)lymphoma, nodal marginal zone B-cell lymphoma, splenic marginal zoneB-cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt'slymphoma, Waldenström's macroglobulinemia (WM, lymphoplasmacyticlymphoma), hairy cell leukemia (HCL), immunoblastic large cell lymphoma,precursor B-lymphoblastic lymphoma, central nervous system (CNS)lymphoma (e.g., primary CNS lymphoma and secondary CNS lymphoma); andT-cell NHL, such as precursor T-lymphoblastic lymphoma/leukemia,peripheral T-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma(CTCL) (e.g., mycosis fungoides, Sezary syndrome), angioimmunoblasticT-cell lymphoma, extranodal natural killer T-cell lymphoma, enteropathytype T-cell lymphoma, subcutaneous panniculitis-like T-cell lymphoma,and anaplastic large cell lymphoma); lymphoma of an immune privilegedsite (e.g., cerebral lymphoma, ocular lymphoma, lymphoma of theplacenta, lymphoma of the fetus, testicular lymphoma); a mixture of oneor more leukemia/lymphoma as described above; myelodysplasia; andmultiple myeloma (MM).

The term “inflammatory disease” refers to a disease caused by, resultingfrom, or resulting in inflammation. The term “inflammatory disease” mayalso refer to a dysregulated inflammatory reaction that causes anexaggerated response by macrophages, granulocytes, and/or T-lymphocytesleading to abnormal tissue damage and/or cell death. An inflammatorydisease can be either an acute or chronic inflammatory condition and canresult from infections or non-infectious causes. Inflammatory diseasesinclude, without limitation, atherosclerosis, arteriosclerosis,autoimmune disorders, multiple sclerosis, systemic lupus erythematosus,polymyalgia rheumatica (PMR), gouty arthritis, degenerative arthritis,tendonitis, bursitis, psoriasis, cystic fibrosis, arthrosteitis,rheumatoid arthritis, inflammatory arthritis, Sjogren's syndrome, giantcell arteritis, progressive systemic sclerosis (scleroderma), ankylosingspondylitis, polymyositis, dermatomyositis, pemphigus, pemphigoid,diabetes (e.g., Type I), myasthenia gravis, Hashimoto's thyroiditis,Graves' disease, Goodpasture's disease, mixed connective tissue disease,sclerosing cholangitis, inflammatory bowel disease, Crohn's disease,ulcerative colitis, pernicious anemia, inflammatory dermatoses, usualinterstitial pneumonitis (UIP), asbestosis, silicosis, bronchiectasis,berylliosis, talcosis, pneumoconiosis, sarcoidosis, desquamativeinterstitial pneumonia, lymphoid interstitial pneumonia, giant cellinterstitial pneumonia, cellular interstitial pneumonia, extrinsicallergic alveolitis, Wegener's granulomatosis and related forms ofangiitis (temporal arteritis and polyarteritis nodosa), inflammatorydermatoses, hepatitis, delayed-type hypersensitivity reactions (e.g.,poison ivy dermatitis), pneumonia, respiratory tract inflammation, AdultRespiratory Distress Syndrome (ARDS), encephalitis, immediatehypersensitivity reactions, asthma, hay fever, allergies, acuteanaphylaxis, rheumatic fever, glomerulonephritis, pyelonephritis,cellulitis, cystitis, chronic cholecystitis, ischemia (ischemic injury),reperfusion injury, allograft rejection, host-versus-graft rejection,appendicitis, arteritis, blepharitis, bronchiolitis, bronchitis,cervicitis, cholangitis, chorioamnionitis, conjunctivitis,dacryoadenitis, dermatomyositis, endocarditis, endometritis, enteritis,enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis,gastritis, gastroenteritis, gingivitis, ileitis, iritis, laryngitis,myelitis, myocarditis, nephritis, omphalitis, oophoritis, orchitis,osteitis, otitis, pancreatitis, parotitis, pericarditis, pharyngitis,pleuritis, phlebitis, pneumonitis, proctitis, prostatitis, rhinitis,salpingitis, sinusitis, stomatitis, synovitis, testitis, tonsillitis,urethritis, urocystitis, uveitis, vaginitis, vasculitis, vulvitis,vulvovaginitis, angitis, chronic bronchitis, osteomyelitis, opticneuritis, temporal arteritis, transverse myelitis, necrotizingfasciitis, and necrotizing enterocolitis.

An “autoimmune disease” refers to a disease arising from aninappropriate immune response of the body of a subject againstsubstances and tissues normally present in the body. In other words, theimmune system mistakes some part of the body as a pathogen and attacksits own cells. This may be restricted to certain organs (e.g., inautoimmune thyroiditis) or involve a particular tissue in differentplaces (e.g., Goodpasture's disease which may affect the basementmembrane in both the lung and kidney). The treatment of autoimmunediseases is typically with immunosuppression, e.g., medications whichdecrease the immune response. Exemplary autoimmune diseases include, butare not limited to, glomerulonephritis, Goodpasture's syndrome,necrotizing vasculitis, lymphadenitis, peri-arteritis nodosa, systemiclupus erythematosis, rheumatoid arthritis, psoriatic arthritis, systemiclupus erythematosis, psoriasis, ulcerative colitis, systemic sclerosis,dermatomyositis/polymyositis, anti-phospholipid antibody syndrome,scleroderma, pemphigus vulgaris, ANCA-associated vasculitis (e.g.,Wegener's granulomatosis, microscopic polyangiitis), uveitis, Sjogren'ssyndrome, Crohn's disease, Reiter's syndrome, ankylosing spondylitis,Lyme disease, Guillain-Barré syndrome, Hashimoto's thyroiditis, andcardiomyopathy.

The term “kinase” is a type of enzyme that transfers phosphate groupsfrom high energy donor molecules, such as ATP, to specific substrates,referred to as phosphorylation. Kinases are part of the larger family ofphosphotransferases. One of the largest groups of kinases are proteinkinases, which act on and modify the activity of specific proteins.Kinases are used extensively to transmit signals and control complexprocesses in cells. Various other kinases act on small molecules such aslipids, carbohydrates, amino acids, and nucleotides, either forsignaling or to prime them for metabolic pathways. Kinases are oftennamed after their substrates. More than 500 different protein kinaseshave been identified in humans. Exemplary human protein kinases include,but are not limited to, AAK1, ABL, ACK, ACTR2, ACTR2B, AKT1, AKT2, AKT3,ALK, ALK1, ALK2, ALK4, ALK7, AMPKa1, AMPKa2, ANKRD3, ANPa, ANPb, ARAF,ARAFps, ARG, AurA, AurAps1, AurAps2, AurB, AurBps1, AurC, AXL, BARK1,BARK2, BIKE, BLK, BMPR1A, BMPR1Aps1, BMPR1Aps2, BMPR1B, BMPR2, BMX,BRAF, BRAFps, BRK, BRSK1, BRSK2, BTK, BUB1, BUBR1, CaMK1a, CaMK1b,CaMK1d, CaMK1g, CaMK2a, CaMK2b, CaMK2d, CaMK2g, CaMK4, CaMKK1, CaMKK2,caMLCK, CASK, CCK4, CCRK, CDC2, CDC7, CDK10, CDK11, CDK2, CDK3, CDK4,CDK4ps, CDK5, CDK5ps, CDK6, CDK7, CDK7ps, CDK8, CDK8ps, CDK9, CDKL1,CDKL2, CDKL3, CDKL4, CDKL5, CGDps, CHED, CHK1, CHK2, CHK2ps1, CHK2ps2,CK1a, CK1a2, CK1aps1, CK1aps2, CK1aps3, CK1d, CK1e, CK1g1, CK1g2,CK1g2ps, CK1g3, CK2a1, CK2a1-rs, CK2a2, CLIK1, CLIK1L, CLK1, CLK2,CLK2ps, CLK3, CLK3ps, CLK4, COT, CRIK, CRK7, CSK, CTK, CYGD, CYGF,DAPK1, DAPK2, DAPK3, DCAMKL1, DCAMKL2, DCAMKL3, DDR1, DDR2, DLK, DMPK1,DMPK2, DRAK1, DRAK2, DYRK1A, DYRK1B, DYRK2, DYRK3, DYRK4, EGFR, EphA1,EphA10, EphA2, EphA3, EphA4, EphA5, EphA6, EphA7, EphA8, EphB1, EphB2,EphB3, EphB4, EphB6, Erk1, Erk2, Erk3, Erk3ps1, Erk3ps2, Erk3ps3,Erk3ps4, Erk4, Erk5, Erk7, FAK, FER, FERps, FES, FGFR1, FGFR2, FGFR3,FGFR4, FGR, FLT1, FLT1ps, FLT3, FLT4, FMS, FRK, Fused, FYN, GAK, GCK,GCN2, GCN22, GPRK4, GPRK5, GPRK6, GPRK6ps, GPRK7, GSK3A, GSK3B, Haspin,HCK, HER2/ErbB2, HER3/ErbB3, HER4/ErbB4, HH498, HIPK1, HIPK2, HIPK3,HIPK4, HPK1, HRI, HRIps, HSER, HUNK, ICK, IGF1R, IKKa, IKKb, IKKe, ILK,INSR, IRAK1, IRAK2, IRAK3, IRAK4, IRE1, IRE2, IRR, ITK, JAK1, JAK2,JAK3, JNK1, JNK2, JNK3, KDR, KHS1, KHS2, KIS, KIT, KSGCps, KSR1, KSR2,LATS1, LATS2, LCK, LIMK1, LIMK2, LIMK2ps, LKB1, LMR1, LMR2, LMR3, LOK,LRRK1, LRRK2, LTK, LYN, LZK, MAK, MAP2K1, MAP2K1ps, MAP2K2, MAP2K2ps,MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K2, MAP3K3, MAP3K4,MAP3K5, MAP3K6, MAP3K7, MAP3K8, MAPKAPK2, MAPKAPK3, MAPKAPK5,MAPKAPKps1, MARK1, MARK2, MARK3, MARK4, MARKps01, MARKps02, MARKps03,MARKps04, MARKps05, MARKps07, MARKps08, MARKps09, MARKps10, MARKps11,MARKps12, MARKps13, MARKps15, MARKps16, MARKps17, MARKps18, MARKps19,MARKps20, MARKps21, MARKps22, MARKps23, MARKps24, MARKps25, MARKps26,MARKps27, MARKps28, MARKps29, MARKps30, MAST1, MAST2, MAST3, MAST4,MASTL, MELK, MER, MET, MISR2, MLK1, MLK2, MLK3, MLK4, MLKL, MNK1,MNK1ps, MNK2, MOK, MOS, MPSK1, MPSK1ps, MRCKa, MRCKb, MRCKps, MSK1,MSK12, MSK2, MSK22, MSSK1, MST1, MST2, MST3, MST3ps, MST4, MUSK, MYO3A,MYO3B, MYT1, NDR1, NDR2, NEK1, NEK10, NEK11, NEK2, NEK2ps1, NEK2ps2,NEK2ps3, NEK3, NEK4, NEK4ps, NEK5, NEK6, NEK7, NEK8, NEK9, NIK, NIM1,NLK, NRBP1, NRBP2, NuaK1, NuaK2, Obscn, Obscn2, OSR1, p38a, p38b, p38d,p38g, p70S6K, p70S6Kb, p70S6Kps1, p70S6Kps2, PAK1, PAK2, PAK2ps, PAK3,PAK4, PAK5, PAK6, PASK, PBK, PCTAIRE1, PCTAIRE2, PCTAIRE3, PDGFRa,PDGFRb, PDK1, PEK, PFTAIRE1, PFTAIRE2, PHKg1, PHKg1ps1, PHKg1ps2,PHKg1ps3, PHKg2, PIK3R4, PIM1, PIM2, PIM3, PINK1, PITSLRE, PKACa, PKACb,PKACg, PKCa, PKCb, PKCd, PKCe, PKCg, PKCh, PKCi, PKCips, PKCt, PKCz,PKD1, PKD2, PKD3, PKG1, PKG2, PKN1, PKN2, PKN3, PKR, PLK1, PLK1ps1,PLK1ps2, PLK2, PLK3, PLK4, PRKX, PRKXps, PRKY, PRP4, PRP4ps, PRPK,PSKH1, PSKH1ps, PSKH2, PYK2, QIK, QSK, RAF1, RAF1ps, RET, RHOK, RIPK1,RIPK2, RIPK3, RNAseL, ROCK1, ROCK2, RON, ROR1, ROR2, ROS, RSK1, RSK12,RSK2, RSK22, RSK3, RSK32, RSK4, RSK42, RSKL1, RSKL2, RYK, RYKps, SAKps,SBK, SCYL1, SCYL2, SCYL2ps, SCYL3, SGK, SgK050ps, SgK069, SgK071,SgK085, SgK110, SgK196, SGK2, SgK223, SgK269, SgK288, SGK3, SgK307,SgK384ps, SgK396, SgK424, SgK493, SgK494, SgK495, SgK496, SIK (e.g.,SIK1, SIK2), skMLCK, SLK, Slob, smMLCK, SNRK, SPEG, SPEG2, SRC, SRM,SRPK1, SRPK2, SRPK2ps, SSTK, STK33, STK33ps, STLK3, STLK5, STLK6,STLK6ps1, STLK6-rs, SuRTK106, SYK, TAK1, TAO1, TAO2, TAO3, TBCK, TBK1,TEC, TESK1, TESK2, TGFbR1, TGFbR2, TIE1, TIE2, TLK1, TLK1ps, TLK2,TLK2ps1, TLK2ps2, TNK1, Trad, Trb1, Trb2, Trb3, Trio, TRKA, TRKB, TRKC,TSSK1, TSSK2, TSSK3, TSSK4, TSSKps1, TSSKps2, TTBK1, TTBK2, TTK, TTN,TXK, TYK2, TYK22, TYRO3, TYRO3ps, ULK1, ULK2, ULK3, ULK4, VACAMKL, VRK1,VRK2, VRK3, VRK3ps, Wee1, Wec1B, Wee1Bps, Wee1ps1, Wee1ps2, Wnk1, Wnk2,Wnk3, Wnk4, YANK1, YANK2, YANK3, YES, YESps, YSK1, ZAK, ZAP70, ZC1/HGK,ZC2/TNIK, ZC3/MINK, and ZC4/NRK.

The term “SRC family kinase” refers to a family of non-receptor tyrosineprotein kinases that includes nine members: SRCA subfamily that includesc-SRC (proto-oncogene tyrosine-protein kinase SRC), YES (proto-oncogenetyrosine-protein kinase Yes), FYN (proto-oncogene tyrosine-proteinkinase FYN), and FGR (Gardner-Rasheed feline sarcoma viral (v-FGR)oncogene homolog); SRCB subfamily that includes LCK (lymphocyte-specificprotein tyrosine kinase), HCK (tyrosine-protein kinase HCK, hemopoieticcell kinase), BLK (tyrosine-protein kinase BLK), and LYN(tyrosine-protein kinase LYN); and FRK (Fyn-related kinase).

The term “CDK” refers to a cyclin-dependent kinase. A CDK binds a cyclin(e.g., Cyclin H), which is a regulatory protein. CDKs phosphorylatetheir substrates at serines and threonines. The consensus sequence forthe phosphorylation site in the amino acid sequence of a CDK substrateis [S/T*]PX[K/R], where S/T* is the phosphorylated serine or threonine,P is proline, X is any amino acid, K is lysine, and R is arginine. CDKsinclude CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10,CDK11, CDK12, CDK13, CDK14, CDK15, CDK16, CDK17, CDK18, CDK19 and CDK20.

CDK7, cyclin-dependent kinase 7, is a CDK, wherein the substrate isCyclin H, MAT1 (e.g., MNAT1), or Cyclin H and MAT1. CDK7 isalternatively referred to as CAK1, HCAK, MO15, STK1, CDKN7, and p39MO15.Non-limiting examples of the nucleotide and protein sequences for humanCDK7 are described in GenBank Accession Number NP_001790, incorporatedherein by reference. The amino acid sequence of this CDK7 is as follows:

MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKL IF

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

Cyclin dependent kinases (CDKs) are key regulators of the cell cycle.Their successive activation and inactivation drives the cycle forward.The activity of CDKs is regulated by multiple mechanisms such aspositive and negative phosphorylation, binding of regulatory proteinslike cyclins, and CDK inhibitors. Cyclin-dependent kinase 7 (CDK7) playsa critical role in the regulation of RNA polymerase II-mediatedtranscription of protein-encoding genes. Disruption of CDK7 signalingcauses defects in transcription; however, a complete understanding ofhow CDK7 disruption affects global transcription is lacking.Furthermore, the absence of selective inhibitors of CDK7 has hinderedinvestigation of the transcriptional and functional consequences ofacute and long-term inhibition of CDK7 under normal and pathologicalconditions. The present invention describes a cellular screen andconventional proteomics target discovery approach that resulted in theidentification of highly selective CDK7 inhibitors and analogs, whichhave the ability to covalently modify a cysteine residue located outsideof the canonical kinase domain (i.e., Cys312 of CDK7). This cysteine isexclusively found in CDK7 and provides an unanticipated means ofovercoming the daunting challenge of achieving selectivity amongst the19 CDKs reported to date. Irreversible inhibition of CDK7 using aninhibitor of the present invention results in the prolonged disruptionof transcription and the induction of apoptosis of a diverse subset ofcancer cell lines. Genome-wide transcript analysis following inhibitortreatment delineates CDK7-responsive genes as important in themaintenance of the cancer cell state, in particular MYC and MCL-1 genes.Selective covalent inhibition of CDK7 may be a viable cancer therapeuticstrategy.

The present invention provides compounds, which inhibit the activity ofa kinase, for the prevention and/or treatment of a subject with aproliferative disease. In certain embodiments, the inventive compoundsinhibit the activity of cyclin-dependent kinase (CDK). In certainembodiments, the inventive compounds inhibit the activity of acyclin-dependent kinase 7 (CDK7). The present invention also providesmethods of using the compounds described herein, e.g., as biologicalprobes to study the inhibition of the activity of a kinase (e.g., CDK(e.g., CDK7)), and as therapeutics, e.g., in the prevention and/ortreatment of diseases associated with the overexpression and/or aberrantactivity of a kinase (e.g., CDK (e.g., CDK7)). In certain embodiments,the diseases are proliferative diseases. The proliferative diseases thatmay be treated and/or prevented include, but are not limited to, cancers(e.g., leukemia, melanoma, multiple myeloma), benign neoplasms, diseasesassociated with angiogenesis, inflammatory diseases, autoinflammatorydiseases, and autoimmune diseases. Also provided by the presentdisclosure are pharmaceutical compositions, kits, methods, and usesincluding a compound of Formula (I) as described herein.

In addition to inhibiting the activity of CDK7, compounds of the presentinvention are selective for CDK7 relative to other CDKs. The presentinvention addresses potential deficiencies of some previous CDK7inhibitors which also have the ability to inhibit CDK12 or CDK13(Kwiatowski et al., “Targeting transcription regulation in cancer with acovalent CDK7 inhibitor.” Nature 511, 616-620 (2014)). This affords theopportunity to more clearly differentiate pharmacological effects thatare derived from CDK7 inhibition relative to CDK12 and/or CDK13inhibition and provides new compounds, and compositions thereof, fordrug development and therapeutic use.

Compounds

Aspects of the present disclosure relate to the compounds describedherein. The compounds described herein are pyrrolo-pyrazole containingcompounds that may be useful in treating and/or preventing proliferativediseases in a subject, inhibiting the activity of a protein kinase(e.g., CDK) in a subject or biological sample, and inducing apoptosis ofa cell. In certain embodiments, a compound described herein is acompound of Formula (I), or a pharmaceutically acceptable salt, solvate,hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopicallylabeled derivative, or prodrug thereof. In certain embodiments, acompound described herein is a compound of Formula (I), or apharmaceutically acceptable salt thereof.

Provided herein are compounds of Formula (I):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein:

-   -   R¹ is —NR^(a)R^(b), —CHR^(a)R^(b) or —OR^(a), wherein each of        R^(a) and R^(b) is independently hydrogen, optionally        substituted alkyl, optionally substituted alkenyl, optionally        substituted alkynyl, optionally substituted carbocyclyl,        optionally substituted heterocyclyl, optionally substituted        aryl, optionally substituted heteroaryl, a nitrogen protecting        group when attached to a nitrogen atom, or an oxygen protecting        group when attached to an oxygen atom, or R^(a) and R^(b) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring;    -   each of R³ and R⁴ is independently hydrogen, halogen, optionally        substituted C₁-C₆ alkyl, or optionally substituted aryl, or R³        and R⁴ are joined to form an optionally substituted C₃-C₆        carbocyclyl ring;    -   R⁵ is independently hydrogen, optionally substituted C₁-C₆        alkyl, or a nitrogen protecting group;    -   L¹ is —NR^(L1)—, —NR^(L1)C(═O)—, —C(═O)NR^(L1)—, —O—, or —S—,        wherein R^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl,        or a nitrogen protecting group;    -   Ring A is optionally substituted carbocyclyl, optionally        substituted heterocyclyl, optionally substituted aryl, or        optionally substituted heteroaryl;    -   L² is a bond, —C(═O)—, —NR^(L2)—, —C(═O)NR^(L2)—,        —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2) is hydrogen,        optionally substituted C₁-C₆ alkyl, or a nitrogen protecting        group;    -   Ring B is absent, optionally substituted carbocyclyl, optionally        substituted heterocyclyl, optionally substituted aryl, or        optionally substituted heteroaryl; and    -   R² is any of Formulae (i-1)-(i-42) as defined herein:

-   -   wherein:    -   L³ is a bond or an optionally substituted C₁₋₄ hydrocarbon        chain, optionally wherein one or more carbon units of the        hydrocarbon chain are independently replaced with —C(═O)—, —O—,        —S—, —NR^(L3a)—, —NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—,        —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—,        trans-CR^(L3b)═CR^(L3b)—, cis-CR^(L3b)═CR^(L3b)—, —C≡C—,        —S(═O)—, —S(═O)O—, —OS(═O)—, —S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—,        —S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L3a)—, or        —NR^(L3a)S(═O)₂—, wherein R^(L3a) is hydrogen, substituted or        unsubstituted C₁₋₆ alkyl, or a nitrogen protecting group, and        wherein each occurrence of R^(L3b) is independently hydrogen,        halogen, optionally substituted alkyl, optionally substituted        alkenyl, optionally substituted alkynyl, optionally substituted        carbocyclyl, optionally substituted heterocyclyl, optionally        substituted aryl, or optionally substituted heteroaryl, or two        R^(L3b) groups are joined to form an optionally substituted        carbocyclic or optionally substituted heterocyclic ring;    -   L⁴ is a bond or an optionally substituted, branched or        unbranched C₁₋₆ hydrocarbon chain; each of R^(E1), R^(E2), and        R^(E3) is independently hydrogen, halogen, optionally        substituted alkyl, optionally substituted alkenyl, optionally        substituted alkynyl, optionally substituted carbocyclyl,        optionally substituted heterocyclyl, optionally substituted        aryl, optionally substituted heteroaryl, —CN, —CH₂OR^(EE),        —CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂,        —Si(R^(EE))₃, and —SR^(EE), wherein each occurrence of R^(EE) is        independently hydrogen, optionally substituted alkyl, optionally        substituted alkoxy, optionally substituted alkenyl, optionally        substituted alkynyl, optionally substituted carbocyclyl,        optionally substituted heterocyclyl, optionally substituted        aryl, or optionally substituted heteroaryl, or two R^(EE) groups        are joined to form an optionally substituted heterocyclic ring;        or R^(E1) and R^(E3), or R^(E2) and R^(E3), or R^(E1) and R^(E2)        are joined to form an optionally substituted carbocyclic or        optionally substituted heterocyclic ring;    -   R^(E4) is a leaving group;    -   R^(E5) is halogen;    -   R^(E6) is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, or        a nitrogen protecting group;    -   each instance of Y is independently O, S, or NR^(E7), wherein        R^(E7) is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, or        a nitrogen protecting group;    -   a is 1 or 2; and    -   each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as        valency permits.

In certain embodiments, a compound described herein is of Formula (I):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein:

-   -   R¹ is —NR^(a)R^(b), —CHR^(a)R^(b) or —OR^(a), wherein each of        R^(a) and R^(b) is independently hydrogen, optionally        substituted alkyl, optionally substituted alkenyl, optionally        substituted alkynyl, optionally substituted carbocyclyl,        optionally substituted heterocyclyl, optionally substituted        aryl, optionally substituted heteroaryl, a nitrogen protecting        group when attached to a nitrogen atom, or an oxygen protecting        group when attached to an oxygen atom, or R^(a) and R^(b) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring;    -   each of R³ and R⁴ is independently hydrogen, halogen, or        optionally substituted C₁-C₆ alkyl, or R³ and R⁴ are joined to        form an optionally substituted C₃-C₆ carbocyclyl ring;    -   R⁵ is hydrogen, optionally substituted C₁-C₆ alkyl, or a        nitrogen protecting group;    -   L¹ is —NR^(L1)—, —NR^(L1)C(═O)—, —C(═O)NR^(L1)—, —O—, or —S—,        wherein R^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl,        or a nitrogen protecting group;    -   Ring A is optionally substituted carbocyclyl, optionally        substituted heterocyclyl, optionally substituted aryl, or        optionally substituted heteroaryl;    -   L² is a bond, —C(═O)—, —NR^(L2)—, —C(═O)NR^(L2)—,        —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2) is hydrogen,        optionally substituted C₁-C₆ alkyl, or a nitrogen protecting        group;    -   Ring B is absent, optionally substituted carbocyclyl, optionally        substituted heterocyclyl, optionally substituted aryl, or        optionally substituted heteroaryl; and    -   R² is any of Formulae (i-1)-(i-41) as defined herein:

-   -   wherein:    -   L³ is a bond or an optionally substituted C₁₋₄ hydrocarbon        chain, optionally wherein one or more carbon units of the        hydrocarbon chain are independently replaced with —C(═O)—, —O—,        —S—, —NR^(L3a)—, —NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—,        —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—,        trans-CR^(L3b)═C^(L3b)—, cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)—,        —S(═O)O—, —OS(═O)—, —S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—, —S(═O)₂—,        —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—,        wherein R^(L3a) is hydrogen, substituted or unsubstituted C₁₋₆        alkyl, or a nitrogen protecting group, and wherein each        occurrence of R^(L3b) is independently hydrogen, halogen,        optionally substituted alkyl, optionally substituted alkenyl,        optionally substituted alkynyl, optionally substituted        carbocyclyl, optionally substituted heterocyclyl, optionally        substituted aryl, or optionally substituted heteroaryl, or two        R^(L3b) groups are joined to form an optionally substituted        carbocyclic or optionally substituted heterocyclic ring;    -   L⁴ is a bond or an optionally substituted, branched or        unbranched C₁₋₆ hydrocarbon chain;    -   each of R^(E1), R^(E2), and R^(E3) is independently hydrogen,        halogen, optionally substituted alkyl, optionally substituted        alkenyl, optionally substituted alkynyl, optionally substituted        carbocyclyl, optionally substituted heterocyclyl, optionally        substituted aryl, optionally substituted heteroaryl, —CN,        —CH₂OR^(EE), —CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂,        —Si(R^(EE))₃, and —SR^(EE), wherein each occurrence of R^(EE) is        independently hydrogen, optionally substituted alkyl, optionally        substituted alkoxy, optionally substituted alkenyl, optionally        substituted alkynyl, optionally substituted carbocyclyl,        optionally substituted heterocyclyl, optionally substituted        aryl, or optionally substituted heteroaryl, or two R^(EE) groups        are joined to form an optionally substituted heterocyclic ring;        or R^(E1) and R^(E3), or R^(E2) and R^(E3), or R^(E1) and R^(E2)        are joined to form an optionally substituted carbocyclic or        optionally substituted heterocyclic ring;    -   R^(E4) is a leaving group;    -   R^(E5) is halogen;    -   R^(E6) is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, or        a nitrogen protecting group;    -   each instance of Y is independently O, S, or NR^(E7), wherein        R^(E7) is hydrogen, substituted or unsubstituted C₁₋₆ alkyl, or        a nitrogen protecting group;    -   a is 1 or 2; and    -   each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as        valency permits.

Compounds of Formula (I) include R¹ attached to the carbonyl substituentof the pyrrolopyrazole bicyclic ring. R¹ may be —NR^(a)R^(b),—CHR^(a)R^(b) or —OR^(a), wherein each of R^(a) and R^(b) isindependently hydrogen, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, or an oxygenprotecting group when attached to an oxygen atom, or R^(a) and R^(b) arejoined to form an optionally substituted carbocyclic, optionallysubstituted heterocyclic, optionally substituted aryl, or optionallysubstituted heteroaryl ring. In certain embodiments, R¹ is —NR^(a)R^(b).In certain embodiments, R¹ is —CHR^(a)R^(b). In certain embodiments, R¹is —OR^(a).

In certain embodiments, R¹ is

wherein R^(2′) is hydrogen, optionally substituted C₁-C₆ alkyl, or anitrogen protecting group, and each ring atom is optionally substituted.In certain embodiments, R¹ is

In certain embodiments, R¹ is of Formula (ii-1):

wherein:

-   -   R^(b) is hydrogen, optionally substituted C₁-C₆ alkyl, or a        nitrogen protecting group;    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   R^(2a) is hydrogen, —OR^(1N), or —NR^(1N)R^(2N), wherein each of        R^(1N) and R^(2N) is independently hydrogen, C₁-C₆ alkyl, a        nitrogen protecting group when attached to a nitrogen atom, or        an oxygen protecting group when attached to an oxygen atom.

In certain embodiments, R¹ is of Formula (ii-2):

wherein:

-   -   R^(b) is hydrogen, optionally substituted C₁-C₆ alkyl, or a        nitrogen protecting group;    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   R^(2a) is hydrogen, —OR^(1N), or —NR^(1N)R^(2N), wherein each of        R^(1N) and R^(2N) is independently hydrogen, C₁-C₆ alkyl, a        nitrogen protecting group when attached to a nitrogen atom, or        an oxygen protecting group when attached to an oxygen atom.

In certain embodiments, R^(b) is hydrogen. In certain embodiments, R^(b)is optionally substituted C₁-C₆ alkyl. In certain embodiments, R^(b) isunsubstituted C₁-C₆ alkyl. In certain embodiments, R^(b) is a nitrogenprotecting group. In certain embodiments, R^(b) is Bn, BOC, Cbz, Fmoc,trifluoroacetyl, triphenylmethyl, acetyl, or Ts.

In certain embodiments, R^(1a) is hydrogen. In certain embodiments,R^(1a) is methyl. In certain embodiments, R^(1a) is ethyl. In certainembodiments, R^(1a) is propyl. In certain embodiments, R^(1a) isoptionally substituted phenyl. In certain embodiments, R^(1a) is phenyl.

In certain embodiments, R^(2a) is hydrogen. In certain embodiments,R^(2a) is —OR^(1N), wherein R^(1N) is hydrogen, C₁-C₆ alkyl, or anoxygen protecting group. In certain embodiments, R^(2a) is —OH. Incertain embodiments, R^(2a) is —NR^(1N)R^(2N), wherein each of R^(1N)and R^(2N) is independently hydrogen, C₁-C₆ alkyl, or a nitrogenprotecting group. In certain embodiments, R^(1N) and R^(2N) are thesame. In certain embodiments, R^(1N) and R^(2N) are distinct. In certainembodiments, R^(1N) and R^(2N) are both methyl. In certain embodiments,R^(1N) and R^(2N) are both ethyl. In certain embodiments, R^(1N) andR^(2N) are both propyl. In certain embodiments, R^(1N) and R^(2N) areboth hydrogen. In certain embodiments, R^(1N) and R^(2N) are bothnitrogen protecting groups. In certain embodiments, at least one ofR^(1N) and R^(2N) is methyl. In certain embodiments, at least one ofR^(1N) and R^(2N) is ethyl. In certain embodiments, at least one ofR^(1N) and R^(2N) is propyl. In certain embodiments, at least one ofR^(1N) and R^(2N) is hydrogen. In certain embodiments, at least one ofR^(1N) and R^(2N) is a nitrogen protecting group. In certainembodiments, R^(1N) is methyl, and R^(2N) is hydrogen. In certainembodiments, R^(1N) is ethyl, and R^(2N) is hydrogen. In certainembodiments, R^(1N) is propyl, and R^(2N) is hydrogen. In certainembodiments, R^(1N) is a nitrogen protecting group, and R^(2N) ishydrogen. In certain embodiments, R^(1N) is methyl, and R^(2N) is anitrogen protecting group. In certain embodiments, R^(1N) is ethyl, andR^(2N) is a nitrogen protecting group. In certain embodiments, R^(1N) ispropyl, and R^(2N) is a nitrogen protecting group.

In certain embodiments, R¹ is of Formula (ii-1a):

wherein:

-   -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group.

In certain embodiments, R¹ is of Formula (ii-2a):

wherein:

-   -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group.

In certain embodiments, R^(1a) is hydrogen. In certain embodiments,R^(1a) is methyl. In certain embodiments, R^(1a) is ethyl. In certainembodiments, R^(1a) is propyl. In certain embodiments, R^(1a) isoptionally substituted phenyl. In certain embodiments, R^(1a) is phenyl.In certain embodiments, R^(1N) and R^(2N) are the same.

In certain embodiments, R^(1N) and R^(2N) are distinct. In certainembodiments, R^(1N) and R^(2N) are both methyl. In certain embodiments,R^(1N) and R^(2N) are both ethyl. In certain embodiments, R^(1N) andR^(2N) are both propyl. In certain embodiments, R^(1N) and R^(2N) areboth hydrogen. In certain embodiments, R^(1N) and R^(2N) are bothnitrogen protecting groups. In certain embodiments, at least one ofR^(1N) and R^(2N) is methyl. In certain embodiments, at least one ofR^(1N) and R^(2N) is ethyl. In certain embodiments, at least one ofR^(1N) and R^(2N) is propyl. In certain embodiments, at least one ofR^(1N) and R^(2N) is hydrogen. In certain embodiments, at least one ofR^(1N) and R^(2N) is a nitrogen protecting group. In certainembodiments, R^(1N) is methyl, and R^(2N) is hydrogen. In certainembodiments, R^(1N) is ethyl, and R^(2N) is hydrogen. In certainembodiments, R^(1N) is propyl, and R^(2N) is hydrogen. In certainembodiments, R^(1N) is a nitrogen protecting group, and R^(2N) ishydrogen. In certain embodiments, R^(1N) is methyl, and R^(2N) is anitrogen protecting group. In certain embodiments, R^(1N) is ethyl, andR^(2N) is a nitrogen protecting group. In certain embodiments, R^(1N) ispropyl, and R^(2N) is a nitrogen protecting group.

In certain embodiments, R¹ is of Formula (ii-1b):

wherein R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, R¹ is of Formula (ii-2b):

wherein R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, R^(1a) is hydrogen. In certain embodiments,R^(1a) is methyl. In certain embodiments, R^(1a) is ethyl. In certainembodiments, R^(1a) is propyl. In certain embodiments, R^(1a) isoptionally substituted phenyl. In certain embodiments, R^(1a) is phenyl.

In certain embodiments, R¹ is:

In certain embodiments, R¹ is:

In certain embodiments, R¹ is:

In certain embodiments, R¹ is:

In certain embodiments, R¹ is of Formula (ii-1c):

wherein:

-   -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or an oxygen protecting group.

In certain embodiments, R¹ is of Formula (ii-2c):

wherein:

-   -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or an oxygen protecting group.

In certain embodiments, R^(1a) is hydrogen. In certain embodiments,R^(1a) is methyl. In certain embodiments, R^(1a) is ethyl. In certainembodiments, R^(1a) is propyl. In certain embodiments, R^(1a) isoptionally substituted phenyl. In certain embodiments, R^(1a) is phenyl.In certain embodiments, R^(1N) is hydrogen. In certain embodiments,R^(1N) is methyl. In certain embodiments, R^(1N) is ethyl. In certainembodiments, R^(1N) is propyl. In certain embodiments, R^(1N) is anoxygen protecting group.

In certain embodiments, R¹ is of Formula (ii-1d):

wherein R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, R¹ is of Formula (ii-2d):

wherein R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, R^(1a) is hydrogen. In certain embodiments,R^(1a) is methyl. In certain embodiments, R^(1a) is ethyl. In certainembodiments, R^(1a) is propyl. In certain embodiments, R^(1a) isoptionally substituted phenyl. In certain embodiments, R^(1a) is phenyl.

In certain embodiments, R¹ is

In certain embodiments, R¹ is —NR^(a)R^(b), wherein R^(a) is optionallysubstituted aryl, and R^(b) is hydrogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl, or anitrogen protecting group. In certain embodiments, R¹ is —NR^(a)R^(b),wherein R^(a) is optionally substituted heteroaryl, and R^(b) ishydrogen, optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl,optionally substituted heteroaryl, or a nitrogen protecting group. Incertain embodiments, R¹ is —NR^(a)R^(b), wherein R^(a) is optionallysubstituted heterocyclyl, and R^(b) is hydrogen, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl, or anitrogen protecting group. In certain embodiments, R¹ is —NR^(a)R^(b),wherein R^(a) is optionally substituted carbocyclyl, and R^(b) isselected from hydrogen, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, or a nitrogenprotecting group. In certain embodiments, R¹ is —NR^(a)R^(b), whereinR^(a) is optionally substituted aryl, and R^(b) is hydrogen. In certainembodiments, R¹ is —NR^(a)R^(b) wherein R^(a) is optionally substitutedheteroaryl, and R^(b) is hydrogen. In certain embodiments, R¹ is—NR^(a)R^(b), wherein R^(a) is optionally substituted heterocyclyl, andR^(b) is hydrogen. In certain embodiments, R¹ is —NR^(a)R^(b), whereinR^(a) is optionally substituted carbocyclyl, and R^(b) is hydrogen. Incertain embodiments, R¹ is —NR^(a)R^(b), wherein R^(a) is optionallysubstituted pyrazolyl, and R^(b) is hydrogen. In certain embodiments, R¹is —NR^(a)R^(b), wherein R^(a) is 1-methyl-1H-pyrazol-4-yl, and R^(b) ishydrogen. In certain embodiments, R¹ is

Compounds of Formula (I) include linker L¹ joining the pyrrolopyrazolebicyclic ring and Ring A. Linker L¹ may be —NR^(L1)—, —NR^(L1)C(═O)—,—C(═O)NR^(L1)—, —O—, or —S—, wherein R^(L1) is hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group. In certainembodiments, L¹ is —NR^(L1)—, wherein R^(L1) is hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protecting group. In certainembodiments, L¹ is —NR^(L1)C(═O)—, wherein R^(L1) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protecting group. Incertain embodiments, L¹ is —C(═O)NR^(L1)—, wherein R^(L1) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protecting group. Incertain embodiments, R^(L1) is hydrogen. In certain embodiments, L¹ is—NH—. In certain embodiments, L¹ is —NH(C═O)—. In certain embodiments,L¹ is —(C═O)NH—. In certain embodiments, L¹ is —O—. In certainembodiments, L¹ is —S—.

Compounds of Formula (I) include R³ and R⁴ attached to thepyrrolopyrazole bicyclic ring. Each of R³ and R⁴ is independentlyhydrogen, halogen, optionally substituted aryl, or optionallysubstituted C₁-C₆ alkyl, or R³ and R⁴ are joined to form an optionallysubstituted C₃-C₆ carbocyclyl ring. In certain embodiments, R³ is asubstituted or unsubstituted aryl (e.g., substituted or unsubstitutedphenyl). In certain embodiments, R⁴ is a substituted or unsubstitutedaryl (e.g., substituted or unsubstituted phenyl). In certainembodiments, R³ and R⁴ are joined to form an optionally substitutedC₃-C₆ carbocyclyl. In certain embodiments, R³ and R⁴ are joined to forman optionally substituted cyclopropane. In certain embodiments, R³ andR⁴ are joined to form an unsubstituted cyclopropane. In certainembodiments, R³ and R⁴ are joined to form an optionally substitutedcyclohexane. In certain embodiments, R³ and R⁴ are joined to form anunsubstituted cyclohexane. In certain embodiments, R³ and R⁴ are thesame. In certain embodiments, R³ and R⁴ are distinct. In certainembodiments, R³ and R⁴ are optionally substituted C₁-C₆ alkyl. Incertain embodiments, R³ and R⁴ are unsubstituted C₁-C₆ alkyl. In certainembodiments, R³ and R⁴ are both methyl. In certain embodiments, R³ andR⁴ are both ethyl. In certain embodiments, R³ and R⁴ are both propyl. Incertain embodiments, R³ and R⁴ are both hydrogen. In certainembodiments, R³ and R⁴ are both halogen. In certain embodiments, each ofR³ and R⁴ is independently —Cl, —Br, or —I. In certain embodiments, R³and R⁴ are both —F. In certain embodiments, R³ and R⁴ are joined as—CH₂CH₂—.

In certain embodiments, R³ is optionally substituted C₁-C₆ alkyl (e.g.,isopropyl). In certain embodiments, R³ is unsubstituted C₁-C₆ alkyl. Incertain embodiments, R³ is methyl. In certain embodiments, R³ is ethyl.In certain embodiments, R³ is propyl. In certain embodiments, R³ ishydrogen. In certain embodiments, R³ is halogen. In certain embodiment,R³ is —Cl, —Br, or —I. In certain embodiment, R³ is —F. In certainembodiments, R⁴ is optionally substituted C₁-C₆ alkyl (e.g., isopropyl).In certain embodiments, R⁴ is unsubstituted C₁-C₆ alkyl. In certainembodiments, R⁴ is methyl. In certain embodiments, R⁴ is ethyl. Incertain embodiments, R⁴ is propyl. In certain embodiments, R⁴ ishydrogen. In certain embodiments, R⁴ is halogen. In certain embodiment,R⁴ is —Cl, —Br, or —I. In certain embodiment, R⁴ is —F.

In certain embodiments, R³ is hydrogen, and R⁴ is methyl. In certainembodiments, R³ is methyl, and R⁴ is hydrogen. In certain embodiments,R³ is hydrogen, and R⁴ is ethyl. In certain embodiments, R³ is ethyl,and R⁴ is hydrogen. In certain embodiments, R³ is hydrogen, and R⁴ ispropyl. In certain embodiments, R³ is propyl, and R⁴ is hydrogen. Incertain embodiments, R³ is hydrogen, and R⁴ is —Cl, —Br, or —I. Incertain embodiments, R³ is —Cl, Br, or —I, and R⁴ is hydrogen. Incertain embodiments, R³ is hydrogen, and R⁴ is —F. In certainembodiments, R³ is —F, and R⁴ is hydrogen. In certain embodiments, R³ ismethyl, and R⁴ is —F. In certain embodiments, R³ is —F, and R⁴ ismethyl. In certain embodiments, R³ is ethyl, and R⁴ is —F. In certainembodiments, R³ is —F, and R⁴ is ethyl. In certain embodiments, R³ ispropyl, and R⁴ is —F. In certain embodiments, R³ is —F, and R⁴ ispropyl. In certain embodiments, R³ is methyl, and R⁴ is —Cl, —Br, or —I.In certain embodiments, R³ is —Cl, —Br, or —I, and R⁴ is methyl. Incertain embodiments, R³ is ethyl, and R⁴ is —Cl, —Br, or —I. In certainembodiments, R³ is —Cl, —Br, or —I, and R⁴ is ethyl. In certainembodiments, R³ is propyl, and R⁴ is —Cl, —Br, or —I. In certainembodiments, R³ is —Cl, —Br, or —I, and R⁴ is propyl.

Compounds of Formula (I) include R⁵ attached to a pyrazole nitrogen. R⁵may be hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group. In certain embodiments, R⁵ is optionally substitutedC₁-C₆ alkyl. In certain embodiments, R⁵ is unsubstituted C₁-C₆ alkyl. Incertain embodiments, R⁵ is substituted methyl. In certain embodiments,R⁵ is unsubstituted methyl. In certain embodiments, R⁵ is hydrogen. Incertain embodiments, R⁵ is a nitrogen protecting group. In certainembodiments, R⁵ is Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl,acetyl, or Ts.

Compounds of Formula (I) may exist as tautomers or mixtures thereof ofFormulae (I-a) and (I-b):

In each tautomer, R⁵ is attached to different pyrazole nitrogens incompounds of each formula. In certain embodiments, R⁵ is attached to thenitrogen at the position labeled 1, as in Formula (I-a). In certainembodiments, R⁵ is attached to the nitrogen at the position labeled 2,as in Formula (I-b). In certain embodiments, compounds of Formula (I)may exist as a mixture of compounds of Formulae (I-a) and (I-b), inwhich case R⁵ is attached to the nitrogen at the position labeled 1 forcomponents of the mixture corresponding to Formula (I-a), and R⁵ is thenitrogen at the position labeled 2 for components of the mixturecorresponding to Formula (I-b).

Compounds of Formula (I) include Ring A between linker L¹ and linker L².Ring A may be optionally substituted carbocyclyl, optionally substitutedheterocyclyl, optionally substituted aryl, or optionally substitutedheteroaryl. In certain embodiments, Ring A is optionally substitutedcarbocyclyl. In certain embodiments, Ring A is optionally substitutedheterocyclyl. In certain embodiments, Ring A is optionally substitutedaryl. In certain embodiments, Ring A is optionally substitutedheteroaryl. In certain embodiments, Ring A is optionally substitutedphenyl. In certain embodiments, Ring A is phenyl substituted with onlyL¹ and L². In certain embodiments, Ring A is optionally substitutedcyclohexyl. In certain embodiments, Ring A is optionally substitutedpiperidinyl. In certain embodiments, Ring A is optionally substitutedpiperizinyl. In certain embodiments, Ring A is optionally substitutedpyridinyl. In certain embodiments, Ring A is optionally substitutedpyrimidinyl.

In certain embodiments, linkers L¹ and L² are attached “ortho” or 1,2 toRing A. In certain embodiments, linkers L¹ and L² are attached “meta” or1,3 to Ring A. In certain embodiments, linkers L¹ and L² are attached“para” or 1,4 to ring A.

In certain embodiments, Ring A is

wherein each ring atom is optionally substituted. In certainembodiments, Ring A is

wherein each ring atom is optionally substituted. In certainembodiments, Ring A is

wherein each ring atom is optionally substituted. In certainembodiments, Ring A is

wherein each ring atom is optionally substituted, and L¹ and L² mayattach to ring A at either indicated position. In certain embodiments,Ring A is

wherein each ring atom is optionally substituted, and L¹ and L² mayattach to ring A at either indicated position. In certain embodiments,Ring A is

wherein each ring atom is optionally substituted, and L¹ and L² mayattach to ring A at either indicated position. In certain embodiments,Ring A is

wherein each ring atom is optionally substituted, and L¹ and L² mayattach to ring A at either indicated position.

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

In certain embodiments, Ring A is

L¹ and L² may attach to ring A at either indicated position. In certainembodiments, Ring A is

wherein L¹ and L² may attach to ring A at either indicated position. Incertain embodiments, Ring A is

wherein L¹ and L² may attach to ring A at either indicated position. Incertain embodiments, Ring A is

wherein L¹ and L² may attach to ring A at either indicated position.

Compounds of Formula (I) include linker L² joining Ring A to Ring B.Linker L² may be a bond, —C(═O)—, —NR^(L2)—, —C(═O)NR^(L2)—,—NR^(L2)C(═O)—, —O—, or —S— wherein R^(L2) is hydrogen, optionallysubstituted C₁-C₆ alkyl, or a nitrogen protection group. In certainembodiments, L² is a bond, such that Ring B or R² is directly attachedto Ring A. In certain embodiments, L² is —NR^(L2)—, wherein R^(L2) ishydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogen protectiongroup. In certain embodiments, L² is —C(═O)NR^(L2)—, wherein R^(L2) ishydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogen protectiongroup. In certain embodiments, L² is —NR^(L2)C(═O)—, wherein R^(L2) ishydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogen protectiongroup. In certain embodiments, L² is —O—. In certain embodiments, L² is—S—. In certain embodiments, R^(L2) is hydrogen. In certain embodiments,L² is —C(═O)—. In certain embodiments, L² is —NH—. In certainembodiments, L² is —NHC(═O)—. In certain embodiments, L² is —C(═O)NH—.In certain embodiments, L² is —O—. In certain embodiments, L² is —S—.

Compounds of Formula (I) include Ring B between linker L² and group R².In certain embodiments, linker L² is a bond, such that Ring B isdirectly attached to Ring A. Ring B may absent, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, or optionally substituted heteroaryl. In certain embodiments, RingB is absent, such that L² is directly attached to R². In certainembodiments, Ring B is absent and linker L² is a bond, such that Ring Ais directly attached to R². In certain embodiments, Ring B is optionallysubstituted carbocyclyl. In certain embodiments, Ring B is optionallysubstituted heterocyclyl. In certain embodiments, Ring B is optionallysubstituted aryl. In certain embodiments, Ring B is optionallysubstituted heteroaryl. In certain embodiments, Ring B is optionallysubstituted phenyl. In certain embodiments, Ring B is optionallysubstituted cyclohexyl. In certain embodiments, Ring B is optionallysubstituted piperidinyl. In certain embodiments, Ring B is optionallysubstituted piperizinyl. In certain embodiments, Ring B is optionallysubstituted pyridinyl. In certain embodiments, Ring B is optionallysubstituted pyrimidinyl.

In certain embodiments, linker L² and group R² are attached “ortho” or1,2 to each other on Ring B. In certain embodiments, linkers L² andgroup R² are attached “meta” or 1,2 to each other on Ring B. In certainembodiments, linkers L² and R² are attached “para” or 1,4 to each otheron Ring B.

In certain embodiments, Ring B is

wherein each ring atom is optionally substituted. In certainembodiments, Ring B is

wherein each ring atom is optionally substituted. In certainembodiments, Ring B is

wherein each ring atom is optionally substituted. In certainembodiments, Ring B is

wherein each ring atom is optionally substituted, and L² and R² mayattach to Ring B at either indicated position. In certain embodiments,Ring B is

wherein each ring atom is optionally substituted, and L² and R² mayattach to Ring B at either indicated position. In certain embodiments,Ring B is

wherein each ring atom is optionally substituted, and L² and R² mayattach to Ring B at either indicated position. In certain embodiments,Ring B is

wherein each ring atom is optionally substituted, and L² and R² mayattach to Ring B at either indicated position.

In certain embodiments, Ring B is

In certain embodiments, Ring B is

In certain embodiments, Ring B is

In certain embodiments, Ring B is

L¹ and L² may attach to Ring B at either indicated position. In certainembodiments, Ring B is

wherein L² and R² may attach to Ring B at either indicated position. Incertain embodiments, Ring B is

wherein L² and R² may attach to Ring B at either indicated position. Incertain embodiments, Ring B is

wherein L² and R² may attach to Ring B at either indicated position.

Compounds of Formula (I) include R² attached to Ring B. In certainembodiments, Ring B is absent, such that R² is directly attached tolinker L². In certain embodiments, Ring B is absent and L² is a bond,such that R² is directly attached to Ring A. In certain embodiments, R²comprises an electrophilic moiety. In certain embodiments, R² comprisesa Michael acceptor moiety. The electrophilic moiety (e.g., Michaelacceptor moiety) may react with a cysteine residue of a kinase (e.g.,CDK (e.g., CDK7)) to allow for covalent attachment of the compound tothe kinase. In certain embodiments, the electrophilic moiety (e.g.,Michael acceptor moiety) may react with a cysteine residue of a kinase(e.g., CDK (e.g., CDK7)). In certain embodiments, the electrophilicmoiety (e.g., Michael acceptor moiety) may react with the Cys312 residueof CDK7. In certain embodiments, the covalent attachment isirreversible. In certain embodiments, the covalent attachment isreversible.

R² may be any one of Formulae (i-1)-(i-42). In certain embodiments, R²is of Formula (i-1):

In certain embodiments, R² is of Formula (i-2):

In certain embodiments, R² is of Formula (i-3):

In certain embodiments, R² is of Formula (i-4):

In certain embodiments, R² is of Formula (i-5):

In certain embodiments, R² is of Formula (i-6):

In certain embodiments, R² is of Formula (i-7):

In certain embodiments, R² is of Formula (i-8):

In certain embodiments, R² is of Formula (i-9):

In certain embodiments, R² is of Formula (i-10):

In certain embodiments, R² is of Formula (i-11):

In certain embodiments, R² is of Formula (i-12):

In certain embodiments, R² is of Formula (i-13):

In certain embodiments, R² is of Formula (i-14):

In certain embodiments, R² is of Formula (i-15):

In certain embodiments, R² is of Formula (i-16):

In certain embodiments, R² is of Formula (i-17):

In certain embodiments, R² is of Formula (i-18):

In certain embodiments, R² is of Formula (i-19):

In certain embodiments, R² is of Formula (i-20):

In certain embodiments, R² is of Formula (i-21):

In certain embodiments, R² is of Formula (i-22):

In certain embodiments, R² is of Formula (i-23):

In certain embodiments, R² is of Formula (i-24):

In certain embodiments, R² is of Formula (i-25):

In certain embodiments, R² is of Formula (i-26):

(i-26). In certain embodiments, R² is of Formula (i 27):

In certain embodiments, R² is of Formula (i-28):

In certain embodiments, R² is of Formula (i-29):

In certain embodiments, R² is of Formula (i-30):

In certain embodiments, R² is of Formula (i-31):

In certain embodiments, R² is of Formula (i-32):

In certain embodiments, R² is of Formula (i-33):

In certain embodiments, R² is of Formula (i-34):

In certain embodiments, R² is of Formula (i-35):

In certain embodiments, R² is of Formula (i-36):

In certain embodiments, R² is of Formula (i-37):

In certain embodiments, R² is of Formula (i-38):

In certain embodiments, R² is of Formula (i-39):

In certain embodiments, R² is of Formula (i-40):

In certain embodiments, R² is of Formula (i-41):

In certain embodiments, R² is of Formula (i-42):

In certain embodiments, R² is of Formula (i-1a):

In certain embodiments, R² is of Formula (i-1b):

In certain embodiments, R² is of Formula (i-1c):

In certain embodiments, R² is of Formula (i-1d)

In certain embodiments, R² is of Formula (i-1e):

In certain embodiments, R² is of Formula (i-1f):

In certain embodiments, R² is of Formula (i-1g):

In certain embodiments, R² is of Formula (i-1g):

In certain embodiments, R² is

In certain embodiments, R² is

In certain embodiments, R² is

In certain embodiments, R² is

In certain embodiments, R² is of Formula (i-1a):

In certain embodiments, R² is of Formula (i-1b):

In certain embodiments, R² is of Formula (i-1c):

In certain embodiments, R² is

In certain embodiments, R² is of Formula (i-18a):

In certain embodiments, R² is of Formula (i-18b):

In certain embodiments, R² is of Formula (i-18c):

In certain embodiments, R² is of Formula (i-15a):

In certain embodiments, R² is of Formula (i-15b):

In certain embodiments, R² is of Formula (i-15c):

R² may contain linker L³ or L⁴. In certain embodiments, L³ is a bond. L³is an optionally substituted C₁₋₄ hydrocarbon chain. In certainembodiments, L³ is optionally substituted ethyl. In certain embodiments,L³ is optionally substituted alkenyl. In certain embodiments, L³ is anoptionally substituted C₁₋₄ hydrocarbon chain, wherein one or morecarbon units of the hydrocarbon chain are independently replaced with—C(═O)—, —O—, —S—, —NR^(L3a)—, —NR^(L3a)C(═)-, —C(═O)NR^(L3a)—,—SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(L3a)C(═S)—,—C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—, cis-CR^(L3b)═CR^(L3b)—,—C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—, —S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—,—S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—.In certain embodiments, L³ is an optionally substituted C₁₋₄ hydrocarbonchain, wherein one carbon unit of the hydrocarbon chain is replaced with—NR^(L3a)— (e.g., —NH—). In certain embodiments, L³ is of the formula:—(CH₂)₁₋₄—NR^(L3a)— (e.g., —(CH₂)₁₋₄—NH—) or —NR^(L3a)—CH₂)₁₋₄— (e.g.,—NH—CH₂)₁₋₄—). In certain embodiments, L³ is —NR^(L3a)—. In certainembodiments, L³ is —NR^(L3a)(C═O)—. In certain embodiments, L³ is—(C═O)NR^(L3a)—. In certain embodiments, L³ is —NH—. In certainembodiments, L³ is —(C═O)—. In certain embodiments, L³ is —NH(C═O)—. Incertain embodiments, L³ is —(C═O)NH—. In certain embodiments, L³ is —O—.In certain embodiments, L³ is —S—. In certain embodiments, L⁴ is a bond.In certain embodiments, L⁴ is an optionally substituted C₁₋₄ hydrocarbonchain.

Linker L³ may contain groups R^(L3a) or R^(L3b). In certain embodiments,R^(L3)a is hydrogen. In certain embodiments, at least one instance ofR^(L3b) is hydrogen. In certain embodiments, each instance of R^(L3b) ishydrogen. In certain embodiments, at least one instance of R^(L3b) is—Cl, —Br, or —I. In certain embodiments, each instance of R^(L3b) is—Cl, —Br, or —I. In certain embodiments, at least one instance ofR^(L3b) is —F. In certain embodiments, each instance of R^(L3b) is —F.In certain embodiments, at least one instance of R^(L3b) is optionallysubstituted alkyl, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl. In certain embodiments, two R^(L3b) groups arejoined to form an optionally substituted carbocyclic or optionallysubstituted heterocyclic ring.

R² may contain groups R^(E1), R^(E2), and/or R^(E3). In certainembodiments, R^(E1) is hydrogen. In certain embodiments, R^(E2) ishydrogen. In certain embodiments, R^(E3) is hydrogen. In certainembodiments, R^(E1) is —Cl, —Br, or —I. In certain embodiments, R^(E2)is —Cl, —Br, or —I. In certain embodiments, R^(E3) is —Cl, —Br, or —I.In certain embodiments, R^(E1) is —F. In certain embodiments, R^(E2) is—F. In certain embodiments, R^(E3) is —F. In certain embodiments, R^(E1)is optionally substituted alkyl (e.g., substituted or unsubstituted C₁₋₆alkyl). In certain embodiments, R^(E2) is optionally substituted alkyl(e.g., substituted or unsubstituted C₁₋₆ alkyl). In certain embodiments,R^(E3) is optionally substituted alkyl (e.g., substituted orunsubstituted C₁₋₆ alkyl). In certain embodiments, R^(E1) is optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, —CN, —CH₂OR^(EE),—CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, or—SR^(EE). In certain embodiments, R^(E2) is optionally substitutedalkenyl, optionally substituted alkynyl, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, optionally substituted heteroaryl, —CN, —CH₂OR^(EE),—CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, or—SR^(EE). In certain embodiments, R^(E3) is optionally substitutedalkenyl, optionally substituted alkynyl, optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, optionally substituted heteroaryl, —CN, —CH₂OR^(EE),—CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂, —Si(R^(EE))₃, or—SR^(EE). In certain embodiments, R^(E1) is —N(R^(EE))₂. In certainembodiments, R^(E2) is —N(R^(EE))₂. In certain embodiments, R^(E3) is—N(R^(EE))₂. In certain embodiments, R^(E1) is —N(CH₃)₂. In certainembodiments, R^(E2) is —N(CH₃)₂. In certain embodiments, R^(E3) is—N(CH₃)₂. In certain embodiments, R^(E1) is —CH₂N(R^(EE))₂. In certainembodiments, R^(E2) is —CH₂N(R^(EE))₂. In certain embodiments, R^(E3) is—CH₂N(R^(EE))₂. In certain embodiments, R^(E1) is —CH₂N(CH₃)₂. Incertain embodiments, R^(E2) is —CH₂N(CH₃)₂. In certain embodiments,R^(E3) is —CH₂N(CH₃)₂. In certain embodiments, R^(E1) is —CN. In certainembodiments, R^(E2) is —CN. In certain embodiments, R^(E3) is —CN.

In certain embodiments, R^(E1) and R^(E3) are joined to form anoptionally substituted carbocyclic ring. In certain embodiments, R^(E1)and R^(E3) are joined to form an optionally substituted heterocyclicring. In certain embodiments, R^(E2) and R^(E3) are joined to form anoptionally substituted carbocyclic ring. In certain embodiments, R^(E2)and R^(E3) are joined to form an optionally substituted heterocyclicring. In certain embodiments, R^(E1) and R^(E2) are joined to form anoptionally substituted carbocyclic ring. In certain embodiments, R^(E1)and R^(E2) are joined to form an optionally substituted heterocyclicring.

R² may contain group R^(E4), where R^(E4) is a leaving group. In certainembodiments, R^(E4) is —Cl, —Br, or —I. In certain embodiments, R^(E4)is —F. In certain embodiments, R^(E4) is —OS(═O)R^(E4a) or—OS(═O)₂R^(E4a), wherein R^(E4a) is substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted carbocyclyl, substituted orunsubstituted heterocyclyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl. In certain embodiments, R^(E4)is —OR^(E4a). In certain embodiments, R^(E4) is -OMs, -OTf, -OTs, -OBs,or 2-nitrobenzenesulfonyloxy. In certain embodiments, R^(E4) is—OR^(E4a). In certain embodiments, R^(E4) is —OMe, —OCF₃, or —OPh. Incertain embodiments, R^(E4) is —OC(═O)R^(E4a). In certain embodiments,R^(E4) is —OC(═O)Me, —OC(═O)CF₃, —OC(═O)Ph, or —OC(═O)Cl. In certainembodiments, R^(E4) is —OC(═O)OR^(E4a). In certain embodiments, R^(E4)is —OC(═O)OMe or —OC(═O)O(t-Bu).

R² may contain group R^(E5), where R^(E5) is a halogen. In certainembodiments, R^(E5) is —Cl, —Br, or —I. In certain embodiments, R^(E5)is —F.

R² may contain group R^(E6). In certain embodiments, R^(E6) is hydrogen.In certain embodiments, R^(E6) is substituted or unsubstituted C₁-C₆alkyl. In certain embodiments, R^(E6) is a nitrogen protecting group.

In certain embodiments, a is 1. In certain embodiments, a is 2.

In certain embodiments, z is 0. In certain embodiments, z is 1. Incertain embodiments, z is 2. In certain embodiments, z is 3, 4, 5, or 6.

R² may contain group Y. In certain embodiments, Y is O. In certainembodiments, Y is S. In certain embodiments, Y is NR^(E7). In certainembodiments, Y is NH.

In certain embodiments, a compound described herein is of Formula (II):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L², Ring A, and Ring B are asdefined for Formula (I).

In certain embodiments, a compound of Formula (I) is of Formula (III):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L², Ring A, and Ring B are asdefined for Formula (I).

In certain embodiments, a compound of Formula (I) is of Formula (IV-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L¹, linker L², and Ring B are asdefined for Formula (I).

In certain embodiments, a compound of Formula (I) is of Formula (IV-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L¹, linker L², and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (IV-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L¹, linker L², and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (IV-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L¹, linker L², and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (IV-e):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L¹, linker L², and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (IV-f):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, R², linker L¹, linker L², and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (V-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L², Ring A, and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (V-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L², Ring A, and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (V-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L², Ring A, and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (V-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L², Ring A, and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁ C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-e):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-f):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-g):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-h):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-j):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-k):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VI-l):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (VII-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L², Ring A, and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VII-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L², Ring A, and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VII-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L², Ring A, and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VII-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L², Ring A, and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-e):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-f):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-g):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-h):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-i):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-j):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-k):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (VIII-l):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof wherein:

-   -   R², linker L¹, linker L², and Ring B are as defined for Formula        (I); and    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl.

In certain embodiments, a compound Formula (I) is of Formula (IX-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, linker L², Ring A, and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (IX-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, linker L², Ring A, and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (IX-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, linker L², Ring A, and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (IX-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein R¹, linker L², Ring A, and Ring B are asdefined for Formula (I).

In certain embodiments, a compound Formula (I) is of Formula (X-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (X-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (X-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (X-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XI-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XI-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XI-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XI-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XII-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XII-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XII-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XII-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XIII-a):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XIII-b):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XIII-c):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, a compound Formula (I) is of Formula (XIII-d):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

-   -   linker L², Ring A, and Ring B are as defined for Formula (I);    -   R^(1a) is hydrogen, C₁-C₆ alkyl, or optionally substituted aryl;        and    -   each of R^(1N) and R^(2N) is independently hydrogen, C₁-C₆        alkyl, or a nitrogen protecting group, or R^(1N) and R^(2N) are        joined to form an optionally substituted carbocyclic, optionally        substituted heterocyclic, optionally substituted aryl, or        optionally substituted heteroaryl ring.

In certain embodiments, the compound according to Formula (I) is acompound listed in Table 1.

TABLE 1 Exemplary Compounds of Formula (I). Name StructureCharacterization Data Compound 101 (S)-3-((3-(4-acrylamidobenzamido)phenyl) amino)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO-d₆) δ 10.44 (d, J = 4.2 Hz, 1H), 10.04 (s, 1H),8.33 (s, 1H), 7.96-7.93 (m, 2H), 7.82-7.80 (m, 2H), 7.34-7.32 (m, 2H),7.26-7.23 (m, 2H), 7.20-7.10 (m, 3H), 6.52-6.46 (m, 1H), 6.35-6.30 (m,1H), 6.09 (s, 1H), 5.84-5.81 (m, 1H), 4.89- 4.83 (m, 1H), 4.35 (d, J =19.8 Hz, 2H), 2.64-2.57 (m, 1H), 2.45-2.38 (m, 1H), 2.18 (s, 6H), 1.65(d, J = 4.2 Hz, 3H), 1.58 (d, J = 4.8 Hz, 3H); MS m/z: 607.4 [M + 1].Compound 102 (S)-3-((4-(4- acrylamidobenzamido)phenyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.46 (s, 1H), 10.01 (s, 1H),8.98-8.89 (br, 1H), 8.25 (s, 1H), 7.99 (d, J = 8.8 Hz, 2H), 7.85 (d, J =8.8 Hz, 2H), 7.64 (d, J = 8.8 Hz, 2H), 7.48-7.42 (m, 4H), 7.38-7.34 (m,1H), 7.00-6.91 (m, 2H), 6.69 (d, J = 8.8 Hz, 1H), 6.53 (dd, J = 17.2,10.0 Hz, 1H), 6.36 (dd, J = 17.2, 2.0 Hz, 1H), 5.87 (dd, J = 10.0, 2.0Hz, 1H), 5.40- 5.35 (m, 1H), 4.48 (d, J = 10.8 Hz, 1H), 4.33 (d, J =10.8 Hz, 1H), 3.10- 2.95 (m, 2H), 2.93 (d, J = 4.8 Hz, 3H), 2.87 (d, J =4.8 Hz, 3H), 1.74 (s, 3H), 1.65 (s, 3H); MS m/z: 607.4 [M + 1]. Compound103 (S)-3-((4-(3- acrylamidobenzamido)phenyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 11.90-11.70 (br, 1H), 10.26 (s,1H), 9.98 (s, 1H), 8.22-8.10 (br, 1H), 8.07 (m, 1H), 7.83 (dd, J = 8.0,1.2 Hz, 1H), 7.57 (d, J = 8.0 Hz, 1H), 7.51 (d, J = 8.8 Hz, 2H), 7.39(t, J = 8.0 Hz, 1H), 7.27 (d, J = 7.2 Hz, 2H), 7.22 (t, J = 7.2 Hz, 2H),7.12 (t, J = 7.2 Hz, 1H), 6.39 (dd, J = 17.2, 10.0 Hz, 1H), 6.22 (dd, J= 17.2, 2.0 Hz, 1H), 6.03-5.92 (m, 1H), 5.72 (dd, J = 10.0, 2.0 Hz, 1H),4.60-4.51 (m, 1H), 4.25-4.14 (m, 2H), 2.52 (dd, J = 12.0, 8.8 Hz, 1H),2.32-2.27 (m, 1H), 2.10 (s, 6H), 1.57 (s, 3H), 1.50 (s, 3H); MS m/z:607.4 [M + l]. Compound 104 (S)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-3-((3- (4-propionamidobenzamido)phenyl)amino)-4,6- dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 12.20-11.80 (br, 1H), 10.09 (s,1H), 9.93 (s, 1H), 8.23 (s, 1H), 7.83 (d, J = 8.0 Hz, 2H), 7.65 (d, J =8.8 Hz, 2H), 7.50-7.30 (m, 1H), 7.27 (d, J = 6.8 Hz, 2H), 7.18 (t, J =7.2 Hz, 2H), 7.13-7.09 (m, 3H), 6.59- 6.51 (m, 1H), 6.12 (s, 1H),4.92-4.80 (m, 1H), 4.29 (s, 2H), 2.30 (q, J = 7.6 Hz, 2H), 2.22 (m, 6H),1.57 (s, 3H), 1.51 (s, 3H), 1.03 (t, J = 7.6 Hz, 3H); MS m/z: 609.4 [M +1]. Compound 105 (S)-3-((3-(3- acrylamidobenzamido)phenyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 12.10-11.82 (br, 1H), 10.26 (s,1H), 10.08 (s, 1H), 8.25 (s, 1H), 8.06 (s, 1H), 7.85 (dd, J = 8.4, 1.2Hz, 1H), 7.55 (d, J = 7.6 Hz, 1H), 7.39 (t, J = 8.0 Hz, 1H), 7.24 (d, J= 7.2 Hz, 2H), 7.15 (t, J = 12 Hz, 2H), 7.08 (d, J = 6.4 Hz, 1H), 6.39(dd, J = 17.2, 10.0 Hz, 1H), 6.22 (dd, J = 17.2, 2.0 Hz, 1H), 5.97 (s,1H), 5.72 (dd, J = 10.0, 2.0 Hz, 1H), 4.76-4.70 (m, 1H), 4.30-4.19 (m,2H), 2.50-2.44 (m, 1H), 2.29-2.22 (m, 1H), 2.05 (s, 6H), 1.57 (s, 3H),1.50 (s, 3H); MS m/z: 607.4 [M + 1]. Compound 106 3-((3-(4-acrylamidobenzamido)phenyl) amimo)-N-(2-(dimethylamino)ethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.49 (s, 1H), 10.07 (s, 1H),9.41 (s, 1H), 8.37 (s, 1H), 7.99 (d, J = 8.8 Hz, 2H), 7.86 (d, J = 8.8Hz, 2H), 7.49 (s, 1H), 7.21 (m, 2H), 6.74 (m, 1H), 6.53 (dd, J = 17.2,10.0 Hz, 1H), 6.38 (m, 1H), 6.36 (dd, J = 17.2, 2.0 Hz, 1H), 5.87 (dd, J= 10.0, 2.0 Hz, 1H), 4.27 (s, 2H), 3.41 (q, J = 5.6 Hz, 2H), 3.18 (q, J= 5.6 Hz, 2H), 2.86 (s, 3H), 2.85 (s, 3H), 1.71 (s, 6H); MS m/z: 531.4[M + 1]. Compound 107 4-acrylamido-N-(3-((6,6- dimethyl-5-(4-methylpiperazine-1- carbonyl)-1,4,5,6- tetrahydropyrrolo[3,4-c]pyrazol-3-yl)amino)phenyl)benzamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.49 (s, 1H), 10.08 (s, 1H),9.68 (s, 1H), 8.44 (s, 1H), 7.99 (d, J = 8.8 Hz, 2H), 7.86 (d, J = 8.4Hz, 2H), 7.62 (s, 1H), 7.23-7.13 (m, 2H), 6.84 (d, J = 7.2 Hz, 1H), 6.53(dd, J = 17.2, 10.0 Hz, 1H), 6.36 (dd, J = 17.2, 2.0 Hz, 1H), 5.87 (dd,J = 10.0, 2.0 Hz, 1H), 4.43 (s, 2H), 3.40- 3.33 (m, 4H), 3.15-2.97 (m,4H), 2.82 (s, 3H), 1.70 (s, 6H); MS m/z: 543.4 [M + 1]. Compound 1083-((3-(4- acrylamidobenzamido)phenyl) amino)-N-(1-(dimethylamino)propan- 2-yl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.35 (s, 1H), 9.95 (s, 1H), 8.91(s, 1H), 8.23 (s, 1H), 7.85 (d, J = 8.4 Hz, 2H), 7.72 (d, J = 8.4 Hz,2H), 7.32 (s, 1H), 7.11-7.05 (m, 2H), 6.57 (m, 1H), 6.40 (dd, J = 16.8,10.0 Hz, 1H), 6.23 (dd, J = 16.8, 2.0 Hz, 1H), 5.91 (d, J = 8.4 Hz, 1H),5.74 (dd, J = 10.0, 2.0 Hz, 1H), 4.18 (s, 2H), 4.14-4.07 (m, 1H),3.05-2.94 (m, 2H), 2.71 (d, J = 4.8 Hz, 3H), 2.69 (d, J = 4.8 Hz, 3H),1.59 (s, 6H), 1.01 (d, J = 6.4 Hz, 3H), 0.85-0.76 (m, 1H); MS m/z: 545.3[M + 1]. Compound 109 (S,E)-3-((3-(4-(4- (dimethylamino)but-2-enamido)benzamido)phenyl) amino)-N-(2-hydroxy-1-phenylethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.68 (s, 1H), 10.13 (s, 1H),10.01 (s, 1H), 8.43 (s, 1H), 8.03 (d, J = 8.8 Hz, 2H), 7.88 (d, J = 8.8Hz, 2H), 7.54 (s, 1H), 7.41-7.39 (m, 2H), 7.34-7.30 (m, 2H), 7.27-7.22(m, 3H), 6.92-6.82 (m, 2H), 6.58 (d, J = 15.6 Hz, 1H), 6.13 (d, J = 8.0Hz, 1H), 4.85 (q, J = 6.8 Hz, 1H), 4.48 (q, J = 11.2 Hz, 2H), 4.06 (d, J= 7.2 Hz, 2H), 3.63 (d, J = 6.4 Hz, 2H), 2.91 (s, 6H), 2.64 (t, J = 5.6Hz, 1H), 1.73 (s, 3H), 1.67 (s, 3H); MS m/z: 637.3 [M + 1]. Compound 110(S)-3-((3- acrylamidophenyl)amino)-N-(2- (dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 9.94 (s, 1H), 8.90 (s, 1H), 8.24(s, 1H), 7.35-7.27 (m, 4H), 7.24-7.22 (m, 2H), 7.08-7.02 (m, 2H),6.56-6.52 (m, 2H), 6.38 (dd, J = 16.8, 10.0 Hz, 1H), 6.16 (dd, J = 16.8,2.0 Hz, 1H), 5.67 (dd, J = 10.0, 2.0 Hz, 1H), 5.29-5.22 (m, 1H), 4.31(q, J = 11.2 Hz, 2H), 3.39-3.34 (m, 1H), 3.28-3.22 (m, 1H), 2.80 (d, J =4.8 Hz, 1H), 2.73 (d, J = 4.8 Hz, 1H), 1.59 (s, 3H), 1.53 (s, 3H); MSm/z: 488.3 [M + 1]. Compound 111 (S)-3-((4-acrylamidophenyl)amino)-N-(2- (dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 9.86 (s, 1H), 8.91 (s, 1H), 8.13(s, 1H), 7.49-7.43 (m, 2H), 7.40-7.27 (m, 5H), 7.22 (m, 1H), 6.82 (d, J= 9.2 Hz, 1H), 6.55 (d, J = 9.2 Hz, 1H), 6.34 (dd, J = 16.8, 10.0 Hz,1H), 6.13 (dd, J = 16.8, 2.0 Hz, 1H), 5.62 (dd, J = 10.0, 2.0 Hz, 1H),5.29- 5.22 (m, 1H), 4.33 (d, J = 11.2 Hz, 1H), 4.19 (d, J = 11.2 Hz,1H), 3.42- 3.36 (m, 1H), 3.29-3.23 (m, 1H), 2.81 (d, J = 4.8 Hz, 1H),2.74 (d, J = 4.8 Hz, 1H), 1.60 (s, 3H), 1.51 (s, 3H); MS m/z: 488.3 [M +1]. Compound 112 (S)-3-(3-(4- acrylamidobenzamido) benzamido)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.97 (s, 1H), 10.53 (s, 1H),10.40 (s, 1H), 9.04 (s, 1H), 8.62 (m, 1H), 8.04 (d, J = 9.2 Hz, 2H),7.89 (d, J = 9.2 Hz, 2H), 7.83 (d, J = 7.6 Hz, 1H), 7.57-7.44 (m, 4H),7.36 (t, J = 7.2 Hz, 1H), 6.83 (d, J = 9.2 Hz, 1H), 6.54 (dd, J = 17.2,10.0 Hz, 1H), 6.37 (dd, J = 17.2, 2.0 Hz, 1H), 5.88 (dd, J = 10.0, 2.0Hz, 1H), 5.43- 5.37 (m, 1H), 4.86 (d, J = 12.4 Hz, 1H), 4.64 (d, J =11.6 Hz, 1H), 2.95 (d, J = 8.4 Hz, 3H), 2.90 (d, J = 8.4 Hz, 3H), 1.74(s, 3 H), 1.66 (s, 3 H); MS m/z: 635.3 [M + 1]. Compound 1133-((R)-1-acryloylpiperidine-3- carboxamido)-N-((S)-2-(dimethylamino)-1-phenylethyl)- 6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 600 MHz (DMSO-d₆) δ 10.56 (d, J = 19.8 Hz, 1H), 8.95(s, 1H), 7.41-7.36 (m, 3H), 7.31-7.27 (m, 1H), 6.87-6.79 (m, 1H), 6.72(d, J = 9.0 Hz, 1H), 6.08 (d, J = 16.2 Hz, 1H), 5.66 (d, J = 10.2 Hz,1H), 5.32 (m, 1H), 4.69 (m, 1H), 4.47 (m, 2H), 4.03 (m, 2H), 3.53 (t, J= 12.0 Hz, 2H), 3.35-3.30 (m, 1H), 3.18-3.12 (m, 1H), 2.99 (t, J = 13.2Hz, 1H), 2.85 (d, J = 5.4 Hz, 3H), 2.82 (d, J = 4.8 Hz, 3H), 2.70 (t, J= 12.0 Hz, 1H), 1.95 (m, 1H), 1.73 (m, 1H), 1.62 (s, 3H), 1.53 (s, 3H),1.33 (m, 1H); MS m/z: 508.3 [M + 1]. Compound 1143-((S)-1-acryloylpiperidine-3- carboxamido)-N-((S)-2-(dimethylamino)-1-phenylethyl)- 6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.50 (d, J = 15.6 Hz, 1H), 8.90(s, 1H), 7.37-7.31 (m, 4H), 7.25-7.21 (m, 1H), 6.82-6.72 (m, 1H), 6.66(d, J = 8.8 Hz, 1H), 6.03 (d, J = 16.4 Hz, 1H), 5.61 (d, J = 10.8 Hz,1H), 5.27 (m, 1H), 4.62 (m, 1H), 4.43 (m, 2H), 4.07-3.96 (m, 2H),3.13-3.05 (m, 2H), 2.94 (t, J = 12.0 Hz, 1H), 2.81 (d, J = 5.2 Hz, 3H),2.77 (d, J = 5.2 Hz, 3H), 2.69-2.57 (m, 1H), 1.89 (m, 1H), 1.67 (m, 1H),1.57 (s, 3H), 1.49 (s, 3H), 1.29 (m, 1H); MS m/z: 508.3 [M + 1].Compound 115 3-((1-(4- acrylamidobenzoyl)piperidin-3-yl)amino)-N-((S)-2- (dimethylamino)-1-phenylethyl)- 6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (TFA salt): 600 MHz (DMSO-d₆) δ 10.29 (s, 1H), 9.10 (s, 1H),7.72-7.55 (m, 1H), 7.49-7.26 (m, 7H), 6.73-6.61 (m, 1H), 6.49-6.40 (m,1H), 6.27-6.24 (m, 1H), 5.77-5.75 (m, 1H), 5.36-5.26 (m, 1H), 4.55-4.50(m, 1H), 4.30-4.24 (m, 2H), 3.55-3.45 (m, 3H), 3.38-3.32 (m, 2H),3.28-3.07 (m, 2H), 2.88 (m, 3H), 2.85 (m, 1H), 2.82 (m, 3H), 2.00-1.90(m, 1H), 1.85-1.70 (m, 1H), 1.65-1.50 (m, 6H), 1.09-1.03 (m, 1H); MSm/z: 599.4 [M + 1]. Compound 116 (S)-3-((1-(4-acrylamidobenzoyl)piperidin-4- yl)amino)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO-d₆) δ 11.30 (br, 1H), 10.30 (s, 1H), 7.71 (d, J =9.0 Hz, 2H), 7.36-7.33 (m, 4H), 7.28 (t, J = 7.8 Hz, 2H), 7.18 (t, J =7.8 Hz, 1H), 6.43 (dd, J = 16.8, 10.2 Hz, 1H), 6.27 (dd, J = 16.8, 2.2Hz, 1H), 5.95 (d, J = 6.0 Hz, 1H), 5.77 (dd, J = 10.2, 2.2 Hz, 1H),5.33-5.20 (m, 1H), 4.82 (q, J = 7.2 Hz, 1H), 4.26 (q, J = 12.0 Hz, 2H),3.72-3.58 (m, 1H), 3.16-3.03 (m, 2H), 2.60 (m, 1H), 2.42 (m, 1H), 2.19(s, 6H), 1.89 (m, 2H), 1.54 (s, 3H), 1.48 (s, 3H), 1.36 (m, 2H); MS m/z:599.4 [M + 1]. Compound 117 3-(((1R,3S)-3-(4- acrylamidobenzamido)cyclohexyl)amino)- N-((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

¹H NMR (TFA salt): 600 MHz (DMSO-d₆) δ 10.35 (d, J = 3.0 Hz, 1H), 9.11(s, 1H), 8.09 (d, J = 7.8 Hz, 1H), 7.80 (dd, J = 9.0, 2.0 Hz, 2H), 7.71(dd, J = 9.0, 1.8 Hz, 2H), 7.46- 7.42 (m, 2H), 7.39-7.35 (m, 2H),7.30-7.28 (m, 1H), 6.68 (t, J = 7.8 Hz, 1H), 6.44 (dd, J = 16.8, 10.2Hz, 1H), 6.27 (dd, J = 16.8, 2.2 Hz, 1H), 5.78 (dd, J = 10.2, 2.2 Hz,1H), 5.34- 5.30 (m, 1H), 4.52 (t, J = 12.0 Hz, 1H), 4.38 (dd, J = 13.2,12.0 Hz, 2H), 4.17-4.10 (m, 1H), 3.67 (m, 2H), 3.48 (t, J = 12.0 Hz,2H), 3.37-3.33 (m, 2H), 2.88 (m, 3H), 2.82 (m, 3H), 1.89-1.80 (m, 2H),1.71-1.60 (m, 3H), 1.62 (s, 3H), 1.55 (s, 3H), 1.36 (m, 2H); MS m/z:613.4 [M + 1]. Compound 118 3-(((1R,3R)-3-(4- acrylamidobenzamido)cyclohexyl)amino)- N-((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO-d₆) δ 11.22 (br, 1H), 10.32 (s, 1H), 8.19 (dd, J =7.8, 3.0 Hz, 1H), 7.81 (dd, J = 8.4, 3.0 Hz, 2H), 7.70 (dd, J = 8.4, 5.4Hz, 2H), 7.35 (d, J = 7.8 Hz, 2H), 7.30-7.26 (m, 2H), 7.20-7.16 (m, 1H),6.43 (dd, J = 16.8, 10.2 Hz, 1H), 6.27 (dd, J = 16.8, 2.2 Hz, 1H), 6.01(m, 1H), 5.77 (dd, J = 10.2, 2.2 Hz, 1H), 5.25-5.17 (m, 1H), 4.89-4.82(m, 1H), 4.36-4.27 (m, 2H), 3.90-3.83 (m, 1H), 3.08-3.01 (m, 1H),2.68-2.60 (m, 1H), 2.50-2.42 (m, 1H), 2.21 (s, 3H), 2.19 (s, 3H),2.13-2.08 (m, 1H), 1.92-1.86 (m, 1H), 1.85-1.79 (m, 1H), 1.78-1.73 (m,1H), 1.54 (s, 3H), 1.48 (d, J = 5.4 Hz, 3H), 1.42-1.35 (m, 1H), 1.28-1.19 (m, 2H), 1.11-1.03 (m, 1H); MS m/z: 613.4 [M + 1]. Compound 119(S)-3-((4-(4- acrylamidobenzamido) cyclohexyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO-d₆) δ 11.30 (br, 1H), 10.32 (s, 1H), 8.11 (d, J =7.8 Hz, 1H), 7.80 (d, J = 8.4 Hz, 2H), 7.71 (d, J = 8.4 Hz, 2H), 7.37(m, 2H), 7.32 (m, 2H), 7.22 (m, 1H), 6.43 (dd, J = 16.8, 10.2 Hz, 1H),6.27 (d, J = 16.8 Hz, 1H), 6.13 (m, 1H), 5.78 (d, J = 10.2, Hz, 1H),5.13-4.94 (m, 2H), 4.35-4.26 (m, 2H), 3.75-3.49 (m, 1H), 3.47 (t, J =5.4 Hz, 1H), 3.40 (t, J = 5.4 Hz, 1H), 3.07-2.97 (m, 2H), 2.50-2.32 (m,4H), 1.98 (d, J = 10.8 Hz, 3H), 1.87 (d, J = 10.2 Hz, 3H), 1.77-1.70 (m,1H), 1.67-1.60 (m, 1H), 1.56 (s, 3H), 1.49 (s, 3H), 1.47- 1.38 (m, 2H),1.37-1.33 (m, 1H), 1.29-1.17 (m, 4H), 1.15 (t, J = 7.2 Hz, 1H),0.85-0.76 (m, 1H); MS m/z: 613.4 [M + 1]. Compound 120

Compound 121

Compound 122

Compound 123

Compound 124

Compound 125

Compound 126

Compound 127

Pharmaceutical Compositions and Administration

The pharmaceutical compositions described herein may be useful intreating and/or preventing proliferative diseases (e.g., cancers (e.g.,leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma,melanoma, multiple myeloma, breast cancer, Ewing's sarcoma,osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectalcancer), benign neoplasms, diseases associated with angiogenesis,inflammatory diseases, autoinflammatory diseases, and autoimmunediseases) in a subject. The compositions described herein may also beuseful for inhibiting the activity of a protein kinase (e.g., CDK (e.g.,CDK7)) in a subject, biological sample, tissue, or cell. Thecompositions described herein may also be useful for inducing apoptosisin a cell.

The present disclosure provides pharmaceutical compositions comprising acompound described herein (e.g., a compound of Formula (I)), or apharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, and optionally a pharmaceutically acceptable excipient.In certain embodiments, the pharmaceutical composition of the inventioncomprises a compound described herein, or a pharmaceutically acceptablesalt thereof, and optionally a pharmaceutically acceptable excipient. Incertain embodiments, a pharmaceutical composition described hereincomprises a compound described herein, or a pharmaceutically acceptablesalt thereof, and a pharmaceutically acceptable excipient. In certainembodiments, the compound described herein, or a pharmaceuticallyacceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer,stereoisomer, isotopically labeled derivative, or prodrug thereof, isprovided in an effective amount in the pharmaceutical composition.

In certain embodiments, the effective amount is a therapeuticallyeffective amount (e.g., amount effective for treating a proliferativedisease in a subject in need thereof). In certain embodiments, theeffective amount is an amount effective for inhibiting the activity of aprotein kinase (e.g., CDK (e.g., CDK7)) in a subject in need thereof. Incertain embodiments, the effective amount is an amount effective forinhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7)) ina cell. In certain embodiments, the effective amount is an amounteffective for inducing apoptosis in a cell. In certain embodiments, theeffective amount is a prophylactically effective amount (e.g., amounteffective for preventing a proliferative disease in a subject in needthereof and/or for keeping a subject in need thereof in remission of aproliferative disease).

In certain embodiments, a protein kinase described herein is a CDK. Incertain embodiments, a protein kinase described herein is CDK1, CDK2,CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK13,CDK14, CDK15, CDK16, CDK17, CDK18, CDK19, or CDK20. In certainembodiments, a protein kinase described herein is CDK7. In certainembodiments, a protein kinase described herein is CDK12. In certainembodiments, a protein kinase described herein is CDK13. In certainembodiments, a protein kinase described herein is a Src family kinase.In certain embodiments, a protein kinase described herein is SRC. Incertain embodiments, a protein kinase described herein is FGR. Incertain embodiments, a protein kinase described herein is BUB1B. Incertain embodiments, a protein kinase described herein is CHEK2. Incertain embodiments, a protein kinase described herein is HIPK4. Incertain embodiments, a protein kinase described herein is PRKCQ. Incertain embodiments, a protein kinase described herein is RET. Incertain embodiments, a protein kinase described herein is MELK. Incertain embodiments, a protein kinase described herein is IRAK1, IRAK4,BMX, or PI3K. In certain embodiments, a protein kinase described hereinis ABL, ARG, BLK, CSK, EphB1, EphB2, FGR, FRK, FYN, SRC, YES, LCK, LYN,MAP2K5, NLK, p38a, SNRK, or TEC. In certain embodiments, a proteinkinase described herein is ABL1(H396P)-phosphorylated,ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, FGR,JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), PDGFRB, SRC,YES, ABL1(H396P)-nonphosphorylated, ABL1(Y253F)-phosphorylated,ABL1-nonphosphorylated, FRK, LYN, ABL1(Q252H)-nonphosphorylated, DDR1,EPHB1, ERBB4, p38-alpha, ABL2, ABL1(Q252H)-phosphorylated, SIK, EPHA8,MEK5, ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN,LCK, EPHA2, ABL1(M351T)-phosphorylated, TXK, EGFR(L858R), EGFR(L861Q),ERBB2, ERBB3, EPHA5, ABL1(F317I)-nonphosphorylated, EGFR(L747-E749del,A750P), CSK, EPHA1, ABL1(F317L)-phosphorylated, BRAF(V600E), EGFR,KIT-autoinhibited, or EGFR(E746-A750del). In certain embodiments, aprotein kinase described herein is ABL1(F317L)-nonphosphorylated,ABL1(H396P)-nonphosphorylated, ABL1(H396P)-phosphorylated,ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4,JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), LYN, PDGFRB,SRC, YES, ABL1-nonphosphorylated, ABL1(Y253F)-phosphorylated, ERBB3,FGR, FRK, p38-alpha, ABL1(F317I)-nonphosphorylated, DDR1, EPHA2,ABL1(Q252H)-phosphorylated, MEK5, ABL1(Q252H)-nonphosphorylated, ABL2,FYN, EPHB1, ABL1(E255K)-phosphorylated, ABL1(F317L)-phosphorylated,EPHA1, ABL1(M351T)-phosphorylated, ERBB4, TXK, LCK, EPHA8, SIK, EPHA5,EGFR(L861Q), CSF1R-autoinhibited, BRAF(V600E), BRK, CSK, KIT(D816V),KIT-autoinhibited, EGFR(L747-T751 del,Sins), EGFR(L858R),EGFR(L747-E749del, A750P), or CSF1R.

In certain embodiments, the effective amount is an amount effective forinhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7)) byat least about 10%, at least about 20%, at least about 30%, at leastabout 40%, at least about 50%, at least about 60%, at least about 70%,at least about 80%, at least about 90%, at least about 95%, or at leastabout 98%. In certain embodiments, the effective amount is an amounteffective for inhibiting the activity of a protein kinase (e.g., CDK(e.g., CDK7)) by not more than 10%, not more than 20%, not more than30%, not more than 40%, not more than 50%, not more than 60%, not morethan 70%, not more than 80%, not more than 90%, not more than 95%, ornot more than 98%. In certain embodiments, the effective amount is anamount effective for inhibiting the activity of a protein kinase (e.g.,CDK (e.g., CDK7)) by a range between a percentage described in thisparagraph and another percentage described in this paragraph, inclusive.

Pharmaceutical compositions described herein can be prepared by anymethod known in the art of pharmacology. In general, such preparatorymethods include bringing the compound described herein (i.e., the“active ingredient”) into association with a carrier or excipient,and/or one or more other accessory ingredients, and then, if necessaryand/or desirable, shaping, and/or packaging the product into a desiredsingle- or multi-dose unit.

Pharmaceutical compositions can be prepared, packaged, and/or sold inbulk, as a single unit dose, and/or as a plurality of single unit doses.A “unit dose” is a discrete amount of the pharmaceutical compositioncomprising a predetermined amount of the active ingredient. The amountof the active ingredient is generally equal to the dosage of the activeingredient which would be administered to a subject and/or a convenientfraction of such a dosage, such as one-half or one-third of such adosage.

Relative amounts of the active ingredient, the pharmaceuticallyacceptable excipient, and/or any additional ingredients in apharmaceutical composition described herein will vary, depending uponthe identity, size, and/or condition of the subject treated and furtherdepending upon the route by which the composition is to be administered.The composition may comprise between 0.1% and 100% (w/w) activeingredient.

Pharmaceutically acceptable excipients used in the manufacture ofprovided pharmaceutical compositions include inert diluents, dispersingand/or granulating agents, surface active agents and/or emulsifiers,disintegrating agents, binding agents, preservatives, buffering agents,lubricating agents, and/or oils. Excipients such as cocoa butter andsuppository waxes, coloring agents, coating agents, sweetening,flavoring, and perfuming agents may also be present in the composition.

Exemplary diluents include calcium carbonate, sodium carbonate, calciumphosphate, dicalcium phosphate, calcium sulfate, calcium hydrogenphosphate, sodium phosphate lactose, sucrose, cellulose,microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodiumchloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.

Exemplary granulating and/or dispersing agents include potato starch,corn starch, tapioca starch, sodium starch glycolate, clays, alginicacid, guar gum, citrus pulp, agar, bentonite, cellulose, and woodproducts, natural sponge, cation-exchange resins, calcium carbonate,silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone)(crospovidone), sodium carboxymethyl starch (sodium starch glycolate),carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose(croscarmellose), methylcellulose, pregelatinized starch (starch 1500),microcrystalline starch, water insoluble starch, calcium carboxymethylcellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate,quaternary ammonium compounds, and mixtures thereof.

Exemplary surface active agents and/or emulsifiers include naturalemulsifiers (e.g., acacia, agar, alginic acid, sodium alginate,tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk,casein, wool fat, cholesterol, wax, and lecithin), colloidal clays(e.g., bentonite (aluminum silicate) and Veegum (magnesium aluminumsilicate)), long chain amino acid derivatives, high molecular weightalcohols (e.g., stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetinmonostearate, ethylene glycol distearate, glyceryl monostearate, andpropylene glycol monostearate, polyvinyl alcohol), carbomers (e.g.,carboxy polymethylene, polyacrylic acid, acrylic acid polymer, andcarboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g.,carboxymethylcellulose sodium, powdered cellulose, hydroxymethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose,methylcellulose), sorbitan fatty acid esters (e.g., polyoxyethylenesorbitan monolaurate (Tween® 20), polyoxyethylene sorbitan (Tween® 60),polyoxyethylene sorbitan monooleate (Tween® 80), sorbitan monopalmitate(Span® 40), sorbitan monostearate (Span® 60), sorbitan tristearate(Span® 65), glyceryl monooleate, sorbitan monooleate (Span® 80),polyoxyethylene esters (e.g., polyoxyethylene monostearate (Myrj® 45),polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil,polyoxymethylene stearate, and Solutol®), sucrose fatty acid esters,polyethylene glycol fatty acid esters (e.g., Cremophor®),polyoxyethylene ethers, (e.g., polyoxyethylene lauryl ether (Brij® 30)),poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamineoleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyllaurate, sodium lauryl sulfate, Pluronic® F-68, poloxamer P-188,cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride,docusate sodium, and/or mixtures thereof.

Exemplary binding agents include starch (e.g., cornstarch and starchpaste), gelatin, sugars (e.g., sucrose, glucose, dextrose, dextrin,molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums(e.g., acacia, sodium alginate, extract of Irish moss, panwar gum,ghatti gum, mucilage of isapol husks, carboxymethylcellulose,methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl methylcellulose, microcrystalline cellulose,cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate(Veegum®), and larch arabogalactan), alginates, polyethylene oxide,polyethylene glycol, inorganic calcium salts, silicic acid,polymethacrylates, waxes, water, alcohol, and/or mixtures thereof.

Exemplary preservatives include antioxidants, chelating agents,antimicrobial preservatives, antifungal preservatives, antiprotozoanpreservatives, alcohol preservatives, acidic preservatives, and otherpreservatives. In certain embodiments, the preservative is anantioxidant. In other embodiments, the preservative is a chelatingagent.

Exemplary antioxidants include alpha tocopherol, ascorbic acid, ascorbylpalmitate, butylated hydroxyanisole, butylated hydroxytoluene,monothioglycerol, potassium metabisulfite, propionic acid, propylgallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, andsodium sulfite.

Exemplary chelating agents include ethylenediaminetetraacetic acid(EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodiumedetate, trisodium edetate, calcium disodium edetate, dipotassiumedetate, and the like), citric acid and salts and hydrates thereof(e.g., citric acid monohydrate), fumaric acid and salts and hydratesthereof, malic acid and salts and hydrates thereof, phosphoric acid andsalts and hydrates thereof, and tartaric acid and salts and hydratesthereof. Exemplary antimicrobial preservatives include benzalkoniumchloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide,cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol,chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea,phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate,propylene glycol, and thimerosal.

Exemplary antifungal preservatives include butyl paraben, methylparaben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoicacid, potassium benzoate, potassium sorbate, sodium benzoate, sodiumpropionate, and sorbic acid.

Exemplary alcohol preservatives include ethanol, polyethylene glycol,phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate,and phenylethyl alcohol.

Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E,beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbicacid, sorbic acid, and phytic acid.

Other preservatives include tocopherol, tocopherol acetate, deteroximemesylate, cetrimide, butylated hydroxyanisol (BHA), butylatedhydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS),sodium lauryl ether sulfate (SLES), sodium bisulfite, sodiummetabisulfite, potassium sulfite, potassium metabisulfite, Glydant®Plus, Phenonip®, methylparaben, Germall® 115, Germaben® II, Neolone®,Kathon®, and Euxyl®.

Exemplary buffering agents include citrate buffer solutions, acetatebuffer solutions, phosphate buffer solutions, ammonium chloride, calciumcarbonate, calcium chloride, calcium citrate, calcium glubionate,calcium gluceptate, calcium gluconate, D-gluconic acid, calciumglycerophosphate, calcium lactate, propanoic acid, calcium levulinate,pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasiccalcium phosphate, calcium hydroxide phosphate, potassium acetate,potassium chloride, potassium gluconate, potassium mixtures, dibasicpotassium phosphate, monobasic potassium phosphate, potassium phosphatemixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodiumcitrate, sodium lactate, dibasic sodium phosphate, monobasic sodiumphosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide,aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline,Ringer's solution, ethyl alcohol, and mixtures thereof.

Exemplary lubricating agents include magnesium stearate, calciumstearate, stearic acid, silica, talc, malt, glyceryl behanate,hydrogenated vegetable oils, polyethylene glycol, sodium benzoate,sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate,sodium lauryl sulfate, and mixtures thereof.

Exemplary natural oils include almond, apricot kernel, avocado, babassu,bergamot, black current seed, borage, cade, camomile, canola, caraway,carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee,corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed,geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate,jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademianut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange,orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed,pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood,sasquana, savoury, sea buckthorn, sesame, shea butter, silicone,soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, andwheat germ oils. Exemplary synthetic oils include, but are not limitedto, butyl stearate, caprylic triglyceride, capric triglyceride,cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate,mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixturesthereof.

Liquid dosage forms for oral and parenteral administration includepharmaceutically acceptable emulsions, microemulsions, solutions,suspensions, syrups and elixirs. In addition to the active ingredients,the liquid dosage forms may comprise inert diluents commonly used in theart such as, for example, water or other solvents, solubilizing agentsand emulsifiers such as ethyl alcohol, isopropyl alcohol, ethylcarbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed,groundnut, corn, germ, olive, castor, and sesame oils), glycerol,tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid estersof sorbitan, and mixtures thereof. Besides inert diluents, the oralcompositions can include adjuvants such as wetting agents, emulsifyingand suspending agents, sweetening, flavoring, and perfuming agents. Incertain embodiments for parenteral administration, the conjugatesdescribed herein are mixed with solubilizing agents such as Cremophor®,alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins,polymers, and mixtures thereof.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions can be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation can be a sterile injectable solution,suspension, or emulsion in a nontoxic parenterally acceptable diluent orsolvent, for example, as a solution in 1,3-butanediol. Among theacceptable vehicles and solvents that can be employed are water,Ringer's solution, U.S.P., and isotonic sodium chloride solution. Inaddition, sterile, fixed oils are conventionally employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or di-glycerides. In addition, fattyacids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, byfiltration through a bacterial-retaining filter, or by incorporatingsterilizing agents in the form of sterile solid compositions which canbe dissolved or dispersed in sterile water or other sterile injectablemedium prior to use.

In order to prolong the effect of a drug, it is often desirable to slowthe absorption of the drug from subcutaneous or intramuscular injection.This can be accomplished by the use of a liquid suspension ofcrystalline or amorphous material with poor water solubility. The rateof absorption of the drug then depends upon its rate of dissolution,which, in turn, may depend upon crystal size and crystalline form.Alternatively, delayed absorption of a parenterally administered drugform may be accomplished by dissolving or suspending the drug in an oilvehicle.

Compositions for rectal or vaginal administration are typicallysuppositories which can be prepared by mixing the conjugates describedherein with suitable non-irritating excipients or carriers such as cocoabutter, polyethylene glycol, or a suppository wax which are solid atambient temperature but liquid at body temperature and therefore melt inthe rectum or vaginal cavity and release the active ingredient.

Solid dosage forms for oral administration include capsules, tablets,pills, powders, and granules. In such solid dosage forms, the activeingredient is mixed with at least one inert, pharmaceutically acceptableexcipient or carrier such as sodium citrate or dicalcium phosphateand/or (a) fillers or extenders such as starches, lactose, sucrose,glucose, mannitol, and silicic acid, (b) binders such as, for example,carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone,sucrose, and acacia, (c) humectants such as glycerol, (d) disintegratingagents such as agar, calcium carbonate, potato or tapioca starch,alginic acid, certain silicates, and sodium carbonate, (e) solutionretarding agents such as paraffin, (f) absorption accelerators such asquaternary ammonium compounds, (g) wetting agents such as, for example,cetyl alcohol and glycerol monostearate, (h) absorbents such as kaolinand bentonite clay, and (i) lubricants such as talc, calcium stearate,magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate,and mixtures thereof. In the case of capsules, tablets, and pills, thedosage form may include a buffering agent.

Solid compositions of a similar type can be employed as fillers in softand hard-filled gelatin capsules using such excipients as lactose ormilk sugar as well as high molecular weight polyethylene glycols and thelike. The solid dosage forms of tablets, dragees, capsules, pills, andgranules can be prepared with coatings and shells such as entericcoatings and other coatings well known in the art of pharmacology. Theymay optionally comprise opacifying agents and can be of a compositionthat they release the active ingredient(s) only, or preferentially, in acertain part of the intestinal tract, optionally, in a delayed manner.Examples of encapsulating compositions which can be used includepolymeric substances and waxes. Solid compositions of a similar type canbe employed as fillers in soft and hard-filled gelatin capsules usingsuch excipients as lactose or milk sugar as well as high molecularweight polyethylene glycols and the like.

The active ingredient can be in a micro-encapsulated form with one ormore excipients as noted above. The solid dosage forms of tablets,dragees, capsules, pills, and granules can be prepared with coatings andshells such as enteric coatings, release controlling coatings, and othercoatings well known in the pharmaceutical formulating art. In such soliddosage forms the active ingredient can be admixed with at least oneinert diluent such as sucrose, lactose, or starch. Such dosage forms maycomprise, as is normal practice, additional substances other than inertdiluents, e.g., tableting lubricants and other tableting aids such amagnesium stearate and microcrystalline cellulose. In the case ofcapsules, tablets and pills, the dosage forms may comprise bufferingagents. They may optionally comprise opacifying agents and can be of acomposition that they release the active ingredient(s) only, orpreferentially, in a certain part of the intestinal tract, optionally,in a delayed manner. Examples of encapsulating agents which can be usedinclude polymeric substances and waxes.

Dosage forms for topical and/or transdermal administration of a compounddescribed herein may include ointments, pastes, creams, lotions, gels,powders, solutions, sprays, inhalants, and/or patches. Generally, theactive ingredient is admixed under sterile conditions with apharmaceutically acceptable carrier or excipient and/or any neededpreservatives and/or buffers as can be required. Additionally, thepresent disclosure contemplates the use of transdermal patches, whichoften have the added advantage of providing controlled delivery of anactive ingredient to the body. Such dosage forms can be prepared, forexample, by dissolving and/or dispensing the active ingredient in theproper medium. Alternatively or additionally, the rate can be controlledby either providing a rate controlling membrane and/or by dispersing theactive ingredient in a polymer matrix and/or gel.

Suitable devices for use in delivering intradermal pharmaceuticalcompositions described herein include short needle devices. Intradermalcompositions can be administered by devices which limit the effectivepenetration length of a needle into the skin. Alternatively oradditionally, conventional syringes can be used in the classical mantouxmethod of intradermal administration. Jet injection devices whichdeliver liquid formulations to the dermis via a liquid jet injectorand/or via a needle which pierces the stratum corneum and produces a jetwhich reaches the dermis are suitable. Ballistic powder/particledelivery devices which use compressed gas to accelerate the compound inpowder form through the outer layers of the skin to the dermis aresuitable.

Formulations suitable for topical administration include, but are notlimited to, liquid and/or semi-liquid preparations such as liniments,lotions, oil-in-water and/or water-in-oil emulsions such as creams,ointments, and/or pastes, and/or solutions and/or suspensions. Topicallyadministrable formulations may, for example, comprise from about 1% toabout 10% (w/w) active ingredient, although the concentration of theactive ingredient can be as high as the solubility limit of the activeingredient in the solvent. Formulations for topical administration mayfurther comprise one or more of the additional ingredients describedherein.

A pharmaceutical composition described herein can be prepared, packaged,and/or sold in a formulation suitable for pulmonary administration viathe buccal cavity. Such a formulation may comprise dry particles whichcomprise the active ingredient and which have a diameter in the rangefrom about 0.5 to about 7 nanometers, or from about 1 to about 6nanometers. Such compositions are conveniently in the form of drypowders for administration using a device comprising a dry powderreservoir to which a stream of propellant can be directed to dispersethe powder and/or using a self-propelling solvent/powder dispensingcontainer such as a device comprising the active ingredient dissolvedand/or suspended in a low-boiling propellant in a sealed container. Suchpowders comprise particles wherein at least 98% of the particles byweight have a diameter greater than 0.5 nanometers and at least 95% ofthe particles by number have a diameter less than 7 nanometers.Alternatively, at least 95% of the particles by weight have a diametergreater than 1 nanometer and at least 90% of the particles by numberhave a diameter less than 6 nanometers. Dry powder compositions mayinclude a solid fine powder diluent such as sugar and are convenientlyprovided in a unit dose form.

Low boiling propellants generally include liquid propellants having aboiling point of below 65° F. at atmospheric pressure. Generally thepropellant may constitute 50 to 99.9% (w/w) of the composition, and theactive ingredient may constitute 0.1 to 20% (w/w) of the composition.The propellant may further comprise additional ingredients such as aliquid non-ionic and/or solid anionic surfactant and/or a solid diluent(which may have a particle size of the same order as particlescomprising the active ingredient).

Pharmaceutical compositions described herein formulated for pulmonarydelivery may provide the active ingredient in the form of droplets of asolution and/or suspension. Such formulations can be prepared, packaged,and/or sold as aqueous and/or dilute alcoholic solutions and/orsuspensions, optionally sterile, comprising the active ingredient, andmay conveniently be administered using any nebulization and/oratomization device. Such formulations may further comprise one or moreadditional ingredients including, but not limited to, a flavoring agentsuch as saccharin sodium, a volatile oil, a buffering agent, a surfaceactive agent, and/or a preservative such as methylhydroxybenzoate. Thedroplets provided by this route of administration may have an averagediameter in the range from about 0.1 to about 200 nanometers.

Formulations described herein as being useful for pulmonary delivery areuseful for intranasal delivery of a pharmaceutical composition describedherein. Another formulation suitable for intranasal administration is acoarse powder comprising the active ingredient and having an averageparticle from about 0.2 to 500 micrometers. Such a formulation isadministered by rapid inhalation through the nasal passage from acontainer of the powder held close to the nares.

Formulations for nasal administration may, for example, comprise fromabout as little as 0.1% (w/w) to as much as 100% (w/w) of the activeingredient, and may comprise one or more of the additional ingredientsdescribed herein. A pharmaceutical composition described herein can beprepared, packaged, and/or sold in a formulation for buccaladministration. Such formulations may, for example, be in the form oftablets and/or lozenges made using conventional methods, and maycontain, for example, 0.1 to 20% (w/w) active ingredient, the balancecomprising an orally dissolvable and/or degradable composition and,optionally, one or more of the additional ingredients described herein.Alternately, formulations for buccal administration may comprise apowder and/or an aerosolized and/or atomized solution and/or suspensioncomprising the active ingredient. Such powdered, aerosolized, and/oraerosolized formulations, when dispersed, may have an average particleand/or droplet size in the range from about 0.1 to about 200 nanometers,and may further comprise one or more of the additional ingredientsdescribed herein.

A pharmaceutical composition described herein can be prepared, packaged,and/or sold in a formulation for ophthalmic administration. Suchformulations may, for example, be in the form of eye drops including,for example, a 0.1-1.0% (w/w) solution and/or suspension of the activeingredient in an aqueous or oily liquid carrier or excipient. Such dropsmay further comprise buffering agents, salts, and/or one or more otherof the additional ingredients described herein. Otheropthalmically-administrable formulations which are useful include thosewhich comprise the active ingredient in microcrystalline form and/or ina liposomal preparation. Ear drops and/or eye drops are alsocontemplated as being within the scope of this disclosure.

Although the descriptions of pharmaceutical compositions provided hereinare principally directed to pharmaceutical compositions which aresuitable for administration to humans, such compositions are generallysuitable for administration to animals of all sorts. Modification ofpharmaceutical compositions suitable for administration to humans inorder to render the compositions suitable for administration to variousanimals is well understood, and the ordinarily skilled veterinarypharmacologist can design and/or perform such modification with ordinaryexperimentation.

The compounds provided herein are typically formulated in dosage unitform for ease of administration and uniformity of dosage. It will beunderstood, however, that the total daily usage of the compositionsdescribed herein will be decided by a physician within the scope ofsound medical judgment. The specific therapeutically effective doselevel for any particular subject or organism will depend upon a varietyof factors including the disease being treated and the severity of thedisorder; the activity of the specific active ingredient employed; thespecific composition employed; the age, body weight, general health,sex, and diet of the subject; the time of administration, route ofadministration, and rate of excretion of the specific active ingredientemployed; the duration of the treatment; drugs used in combination orcoincidental with the specific active ingredient employed; and likefactors well known in the medical arts.

The compounds and compositions provided herein can be administered byany route, including enteral (e.g., oral), parenteral, intravenous,intramuscular, intra-arterial, intramedullary, intrathecal,subcutaneous, intraventricular, transdermal, interdermal, rectal,intravaginal, intraperitoneal, topical (as by powders, ointments,creams, and/or drops), mucosal, nasal, bucal, sublingual; byintratracheal instillation, bronchial instillation, and/or inhalation;and/or as an oral spray, nasal spray, and/or aerosol. Specificallycontemplated routes are oral administration, intravenous administration(e.g., systemic intravenous injection), regional administration viablood and/or lymph supply, and/or direct administration to an affectedsite. In general, the most appropriate route of administration willdepend upon a variety of factors including the nature of the agent(e.g., its stability in the environment of the gastrointestinal tract),and/or the condition of the subject (e.g., whether the subject is ableto tolerate oral administration). In certain embodiments, the compoundor pharmaceutical composition described herein is suitable for topicaladministration to the eye of a subject.

The exact amount of a compound required to achieve an effective amountwill vary from subject to subject, depending, for example, on species,age, and general condition of a subject, severity of the side effects ordisorder, identity of the particular compound, mode of administration,and the like. An effective amount may be included in a single dose(e.g., single oral dose) or multiple doses (e.g., multiple oral doses).In certain embodiments, when multiple doses are administered to asubject or applied to a biological sample, tissue, or cell, any twodoses of the multiple doses include different or substantially the sameamounts of a compound described herein. In certain embodiments, whenmultiple doses are administered to a subject or applied to a biologicalsample, tissue, or cell, the frequency of administering the multipledoses to the subject or applying the multiple doses to the tissue orcell is three doses a day, two doses a day, one dose a day, one doseevery other day, one dose every third day, one dose every week, one doseevery two weeks, one dose every three weeks, or one dose every fourweeks. In certain embodiments, the frequency of administering themultiple doses to the subject or applying the multiple doses to thetissue or cell is one dose per day. In certain embodiments, thefrequency of administering the multiple doses to the subject or applyingthe multiple doses to the tissue or cell is two doses per day. Incertain embodiments, the frequency of administering the multiple dosesto the subject or applying the multiple doses to the tissue or cell isthree doses per day. In certain embodiments, when multiple doses areadministered to a subject or applied to a biological sample, tissue, orcell, the duration between the first dose and last dose of the multipledoses is one day, two days, four days, one week, two weeks, three weeks,one month, two months, three months, four months, six months, ninemonths, one year, two years, three years, four years, five years, sevenyears, ten years, fifteen years, twenty years, or the lifetime of thesubject, biological sample, tissue, or cell. In certain embodiments, theduration between the first dose and last dose of the multiple doses isthree months, six months, or one year. In certain embodiments, theduration between the first dose and last dose of the multiple doses isthe lifetime of the subject, biological sample, tissue, or cell. Incertain embodiments, a dose (e.g., a single dose, or any dose ofmultiple doses) described herein includes independently between 0.1 μgand 1 μg, between 0.001 mg and 0.01 mg, between 0.01 mg and 0.1 mg,between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg,between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and300 mg, between 300 mg and 1,000 mg, or between 1 g and 10 g, inclusive,of a compound described herein. In certain embodiments, a dose describedherein includes independently between 1 mg and 3 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 3 mg and 10 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 10 mg and 30 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 30 mg and 100 mg, inclusive, of acompound described herein.

Dose ranges as described herein provide guidance for the administrationof provided pharmaceutical compositions to an adult. The amount to beadministered to, for example, a child or an adolescent can be determinedby a medical practitioner or person skilled in the art and can be loweror the same as that administered to an adult.

A compound or composition, as described herein, can be administered incombination with one or more additional pharmaceutical agents (e.g.,therapeutically and/or prophylactically active agents) useful intreating and/or preventing a proliferative disease. The compounds orcompositions can be administered in combination with additionalpharmaceutical agents that improve their activity (e.g., activity (e.g.,potency and/or efficacy) in treating a proliferative disease in asubject in need thereof, in preventing a proliferative disease in asubject in need thereof, and/or in inhibiting the activity of a proteinkinase (e.g., CDK (e.g., CDK7) in a subject, biological sample, tissue,or cell), improve bioavailability, improve safety, reduce drugresistance, reduce and/or modify metabolism, inhibit excretion, and/ormodify distribution in a subject, biological sample, tissue, or cell. Itwill also be appreciated that the therapy employed may achieve a desiredeffect for the same disorder, and/or it may achieve different effects.In certain embodiments, a pharmaceutical composition described hereinincluding a compound described herein and an additional pharmaceuticalagent shows a synergistic effect that is absent in a pharmaceuticalcomposition including one of the compound and the additionalpharmaceutical agent, but not both.

The compound or composition can be administered concurrently with, priorto, or subsequent to one or more additional pharmaceutical agents, whichmay be useful as, e.g., combination therapies in treating and/orpreventing a proliferative disease. Pharmaceutical agents includetherapeutically active agents. Pharmaceutical agents also includeprophylactically active agents. Pharmaceutical agents include smallorganic molecules such as drug compounds (e.g., compounds approved forhuman or veterinary use by the U.S. Food and Drug Administration asprovided in the Code of Federal Regulations (CFR)), peptides, proteins,carbohydrates, monosaccharides, oligosaccharides, polysaccharides,nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides orproteins, small molecules linked to proteins, glycoproteins, steroids,nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides,antisense oligonucleotides, lipids, hormones, vitamins, and cells. Incertain embodiments, the additional pharmaceutical agent is apharmaceutical agent useful in treating a proliferative disease. Incertain embodiments, the additional pharmaceutical agent is apharmaceutical agent useful in preventing a proliferative disease. Incertain embodiments, the additional pharmaceutical agent is apharmaceutical agent useful in inhibiting the activity of a proteinkinase (e.g., CDK (e.g., CDK7)) in a subject, biological sample, tissue,or cell. In certain embodiments, the additional pharmaceutical agent isa pharmaceutical agent useful in inducing apoptosis in a cell. Incertain embodiments, the additional pharmaceutical agent is apharmaceutical agent approved by a regulatory agency (e.g., the US FDA)for treating and/or preventing a proliferative disease. Each additionalpharmaceutical agent may be administered at a dose and/or on a timeschedule determined for that pharmaceutical agent. The additionalpharmaceutical agent(s) may also be administered together with eachother and/or with the compound or composition described herein in asingle dose or administered separately in different doses. Theparticular combination to employ in a regimen will take into accountcompatibility of the compound described herein with the additionalpharmaceutical agent(s) and/or the desired therapeutic and/orprophylactic effect to be achieved. In general, it is expected that theadditional pharmaceutical agent(s) in combination be utilized at levelsthat do not exceed the levels at which they are utilized individually.In some embodiments, the levels utilized in combination will be lowerthan those utilized individually.

In certain embodiments, the additional pharmaceutical agent is ananti-proliferative agent (e.g., anti-cancer agent). In certainembodiments, the additional pharmaceutical agent is an anti-leukemiaagent. In certain embodiments, the additional pharmaceutical agent isABITREXATE (methotrexate), ADE, Adriamycin RDF (doxorubicinhydrochloride), Ambochlorin (chlorambucil), ARRANON (nelarabine),ARZERRA (ofatumumab), BOSULIF (bosutinib), BUSULFEX (busulfan), CAMPATH(alemtuzumab), CERUBIDINE (daunorubicin hydrochloride), CLAFEN(cyclophosphamide), CLOFAREX (clofarabine), CLOLAR (clofarabine), CVP,CYTOSAR-U (cytarabine), CYTOXAN (cyclophosphamide), ERWINAZE(Asparaginase Erwinia Chrysanthemi), FLUDARA (fludarabine phosphate),FOLEX (methotrexate), FOLEX PFS (methotrexate), GAZYVA (obinutuzumab),GLEEVEC (imatinib mesylate), Hyper-CVAD, ICLUSIG (ponatinibhydrochloride), IMBRUVICA (ibrutinib), LEUKERAN (chlorambucil),LINFOLIZIN (chlorambucil), MARQIBO (vincristine sulfate liposome),METHOTREXATE LPF (methorexate), MEXATE (methotrexate), MEXATE-AQ(methotrexate), mitoxantrone hydrochloride, MUSTARGEN (mechlorethaminehydrochloride), MYLERAN (busulfan), NEOSAR (cyclophosphamide), ONCASPAR(Pegaspargase), PURINETHOL (mercaptopurine), PURIXAN (mercaptopurine),Rubidomycin (daunorubicin hydrochloride), SPRYCEL (dasatinib), SYNRIBO(omacetaxine mepesuccinate), TARABINE PFS (cytarabine), TASIGNA(nilotinib), TREANDA (bendamustine hydrochloride), TRISENOX (arsenictrioxide), VINCASAR PFS (vincristine sulfate), ZYDELIG (idelalisib), ora combination thereof. In certain embodiments, the additionalpharmaceutical agent is an anti-lymphoma agent. In certain embodiments,the additional pharmaceutical agent is ABITREXATE (methotrexate), ABVD,ABVE, ABVE-PC, ADCETRIS (brentuximab vedotin), ADRIAMYCIN PFS(doxorubicin hydrochloride), ADRIAMYCIN RDF (doxorubicin hydrochloride),AMBOCHLORIN (chlorambucil), AMBOCLORIN (chlorambucil), ARRANON(nelarabine), BEACOPP, BECENUM (carmustine), BELEODAQ (belinostat),BEXXAR (tositumomab and iodine I 131 tositumomab), BICNU (carmustine),BLENOXANE (bleomycin), CARMUBRIS (carmustine), CHOP, CLAFEN(cyclophosphamide), COPP, COPP-ABV, CVP, CYTOXAN (cyclophosphamide),DEPOCYT (liposomal cytarabine), DTIC-DOME (dacarbazine), EPOCH, FOLEX(methotrexate), FOLEX PFS (methotrexate), FOLOTYN (pralatrexate),HYPER-CVAD, ICE, IMBRUVICA (ibrutinib), INTRON A (recombinant interferonalfa-2b), ISTODAX (romidepsin), LEUKERAN (chlorambucil), LINFOLIZIN(chlorambucil), Lomustine, MATULANE (procarbazine hydrochloride),METHOTREXATE LPF (methotrexate), MEXATE (methotrexate), MEXATE-AQ(methotrexate), MOPP, MOZOBIL (plerixafor), MUSTARGEN (mechlorethaminehydrochloride), NEOSAR (cyclophosphamide), OEPA, ONTAK (denileukindiftitox), OPPA, R-CHOP, REVLIMID (lenalidomide), RITUXAN (rituximab),STANFORD V, TREANDA (bendamustine hydrochloride), VAMP, VELBAN(vinblastine sulfate), VELCADE (bortezomib), VELSAR (vinblastinesulfate), VINCASAR PFS (vincristine sulfate), ZEVALIN (ibritumomabtiuxetan), ZOLINZA (vorinostat), ZYDELIG (idelalisib), or a combinationthereof. In certain embodiments, the additional pharmaceutical agent isan anti-myelodysplasia agent. In certain embodiments, the additionalpharmaceutical agent is REVLIMID (lenalidomide), DACOGEN (decitabine),VIDAZA (azacitidine), CYTOSAR-U (cytarabine), IDAMYCIN (idarubicin),CERUBIDINE (daunorubicin), or a combination thereof.

In certain embodiments, the additional pharmaceutical agent is ananti-macroglobulinemia agent.

In certain embodiments, the additional pharmaceutical agent is LEUKERAN(chlorambucil), NEOSAR (cyclophosphamide), FLUDARA (fludarabine),LEUSTATIN (cladribine), or a combination thereof. In certainembodiments, the additional pharmaceutical agent is ABITREXATE(methotrexate), ABRAXANE (paclitaxel albumin-stabilized nanoparticleformulation), AC, AC-T, ADE, ADRIAMYCIN PFS (doxorubicin hydrochloride),ADRUCIL (fluorouracil), AFINITOR (everolimus), AFINITOR DISPERZ(everolimus), ALDARA (imiquimod), ALIMTA (pemetrexed disodium), AREDIA(pamidronate disodium), ARIMIDEX (anastrozole), AROMASIN (exemestane),AVASTIN (bevacizumab), BECENUM (carmustine), BEP, BICNU (carmustine),BLENOXANE (bleomycin), CAF, CAMPTOSAR (irinotecan hydrochloride), CAPOX,CAPRELSA (vandetanib), CARBOPLATIN-TAXOL, CARMUBRIS (carmustine),CASODEX (bicalutamide), CEENU (lomustine), CERUBIDINE (daunorubicinhydrochloride), CERVARIX (recombinant HPV bivalent vaccine), CLAFEN(cyclophosphamide), CMF, COMETRIQ (cabozantinib-s-malate), COSMEGEN(dactinomycin), CYFOS (ifosfamide), CYRAMZA (ramucirumab), CYTOSAR-U(cytarabine), CYTOXAN (cyclophosphamide), DACOGEN (decitabine),DEGARELIX, DOXIL (doxorubicin hydrochloride liposome), DOXORUBICINHYDROCHLORIDE, DOX-SL (doxorubicin hydrochloride liposome), DTIC-DOME(dacarbazine), EFUDEX (fluorouracil), ELLENCE (epirubicinhydrochloride), ELOXATIN (oxaliplatin), ERBITUX (cetuximab), ERIVEDGE(vismodegib), ETOPOPHOS (etoposide phosphate), EVACET (doxorubicinhydrochloride liposome), FARESTON (toremifene), FASLODEX (fulvestrant),FEC, FEMARA (letrozole), FLUOROPLEX (fluorouracil), FOLEX(methotrexate), FOLEX PFS (methotrexate), FOLFIRI, FOLFIRI-BEVACIZUMAB,FOLFIRI-CETUXIMAB, FOLFIRINOX, FOLFOX, FU-LV, GARDASIL (recombinanthuman papillomavirus (HPV) quadrivalent vaccine), GEMCITABINE-CISPLATIN,GEMCITABINE-OXALIPLATIN, GEMZAR (gemcitabine hydrochloride), GILOTRIF(afatinib dimaleate), GLEEVEC (imatinib mesylate), GLIADEL (carmustineimplant), GLIADEL WAFER (carmustine implant), HERCEPTIN (trastuzumab),HYCAMTIN (topotecan hydrochloride), IFEX (ifosfamide), IFOSFAMIDUM(ifosfamide), INLYTA (axitinib), INTRON A (recombinant interferonalfa-2b), IRESSA (gefitinib), IXEMPRA (ixabepilone), JAKAFI (ruxolitinibphosphate), JEVTANA (cabazitaxel), KADCYLA (ado-trastuzumab emtansine),KEYTRUDA (pembrolizumab), KYPROLIS (carfilzomib), LIPODOX (doxorubicinhydrochloride liposome), LUPRON (leuprolide acetate), LUPRON DEPOT(leuprolide acetate), LUPRON DEPOT-3 MONTH (leuprolide acetate), LUPRONDEPOT-4 MONTH (leuprolide acetate), LUPRON DEPOT-PED (leuprolideacetate), MEGACE (megestrol acetate), MEKINIST (trametinib),METHAZOLASTONE (temozolomide), METHOTREXATE LPF (methotrexate), MEXATE(methotrexate), MEXATE-AQ (methotrexate), MITOXANTRONE HYDROCHLORIDE,MITOZYTREX (mitomycin c), MOZOBIL (plerixafor), MUSTARGEN(mechlorethamine hydrochloride), MUTAMYCIN (mitomycin c), MYLOSAR(azacitidine), NAVELBINE (vinorelbine tartrate), NEOSAR(cyclophosphamide), NEXAVAR (sorafenib tosylate), NOLVADEX (tamoxifencitrate), NOVALDEX (tamoxifen citrate), OFF, PAD, PARAPLAT(carboplatin), PARAPLATIN (carboplatin), PEG-INTRON (peginterferonalfa-2b), PEMETREXED DISODIUM, PERJETA (pertuzumab), PLATINOL(cisplatin), PLATINOL-AQ (cisplatin), POMALYST (pomalidomide),prednisone, PROLEUKIN (aldesleukin), PROLIA (denosumab), PROVENGE(sipuleucel-t), REVLIMID (lenalidomide), RUBIDOMYCIN (daunorubicinhydrochloride), SPRYCEL (dasatinib), STIVARGA (regorafenib), SUTENT(sunitinib malate), SYLATRON (peginterferon alfa-2b), SYLVANT(siltuximab), SYNOVIR (thalidomide), TAC, TAFINLAR (dabrafenib),TARABINE PFS (cytarabine), TARCEVA (erlotinib hydrochloride), TASIGNA(nilotinib), TAXOL (paclitaxel), TAXOTERE (docetaxcl), TEMODAR(temozolomide), THALOMID (thalidomide), TOPOSAR (etoposide), TORISEL(temsirolimus), TPF, TRISENOX (arsenic trioxide), TYKERB (lapatinibditosylate), VECTIBIX (panitumumab), VEIP, VELBAN (vinblastine sulfate),VELCADE (bortezomib), VELSAR (vinblastine sulfate), VEPESID (etoposide),VIADUR (leuprolide acetate), VIDAZA (azacitidine), VINCASAR PFS(vincristine sulfate), VOTRIENT (pazopanib hydrochloride), WELLCOVORIN(leucovorin calcium), XALKORI (crizotinib), XELODA (capecitabine),XELOX, XGEVA (denosumab), XOFIGO (radium 223 dichloride), XTANDI(enzalutamide), YERVOY (ipilimumab), ZALTRAP (ziv-aflibercept), ZELBORAF(vemurafenib), ZOLADEX (goserelin acetate), ZOMETA (zoledronic acid),ZYKADIA (ceritinib), ZYTIGA (abiraterone acetate), or a combinationthereof. In certain embodiments, the additional pharmaceutical agent isa protein kinase inhibitor (e.g., tyrosine protein kinase inhibitor). Incertain embodiments, the additional pharmaceutical agent is an inhibitorof a Src family kinase. In certain embodiments, the additionalpharmaceutical agent is a CDK inhibitor. In certain embodiments, theadditional pharmaceutical agent is a CDK7 inhibitor. In certainembodiments, the additional pharmaceutical agent is an inhibitor of oneor more protein kinases selected from the group consisting of IRAK1,IRAK4, BMX, and PI3K. In certain embodiments, the additionalpharmaceutical agent is an inhibitor of one or more protein kinasesselected from the group consisting of BUB1B, CDK2, CDK9, CHEK2, FGR,HIPK4, PRKCQ, RET, SRC, or MELK. In certain embodiments, the additionalpharmaceutical agent is an inhibitor of one or more protein kinasesselected from the group consisting of ABL, ARG, BLK, CSK, EphB1, EphB2,FGR, FRK, FYN, SRC, YES, LCK, LYN, MAP2K5, NLK, p38a, SNRK, and TEC. Incertain embodiments, the additional pharmaceutical agent is an inhibitorof one or more protein kinases selected from the group consisting ofABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2,EPHB3, EPHB4, FGR, JAK3(JH1domain-catalytic), KIT, KIT(L576P),KIT(V559D), PDGFRB, SRC, YES, ABL1(H396P)-nonphosphorylated,ABL1(Y253F)-phosphorylated, ABL1-nonphosphorylated, FRK, LYN,ABL1(Q252H)-nonphosphorylated, DDR1, EPHB1, ERBB4, p38-alpha, ABL2,ABL1(Q252H)-phosphorylated, SIK, EPHA8, MEK5,ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN, LCK,EPHA2, ABL1(M351T)-phosphorylated, TXK, EGFR(L858R), EGFR(L861Q), ERBB2,ERBB3, EPHA5, ABL1(F317I)-nonphosphorylated, EGFR(L747-E749del, A750P),CSK, EPHA1, ABL1(F317L)-phosphorylated, BRAF(V600E), EGFR,KIT-autoinhibited, and EGFR(E746-A750del). In certain embodiments, theadditional pharmaceutical agent is an inhibitor of one or more proteinkinases selected from the group consisting ofABL1(F317L)-nonphosphorylated, ABL1(H396P)-nonphosphorylated,ABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2,EPHB3, EPHB4, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D),LYN, PDGFRB, SRC, YES, ABL1-nonphosphorylated,ABL1(Y253F)-phosphorylated, ERBB3, FGR, FRK, p38-alpha,ABL1(F317I)-nonphosphorylated, DDR1, EPHA2, ABL1(Q252H)-phosphorylated,MEK5, ABL1(Q252H)-nonphosphorylated, ABL2, FYN, EPHB1,ABL1(E255K)-phosphorylated, ABL1(F317L)-phosphorylated, EPHA1,ABL1(M351T)-phosphorylated, ERBB4, TXK, LCK, EPHA8, SIK, EPHA5,EGFR(L861Q), CSF1R-autoinhibited, BRAF(V600E), BRK, CSK, KIT(D816V),KIT-autoinhibited, EGFR(L747-T751del,Sins), EGFR(L858R),EGFR(L747-E749del, A750P), and CSF1R. In certain embodiments, theadditional pharmaceutical agent is an anti-angiogenesis agent,anti-inflammatory agent, immunosuppressant, anti-bacterial agent,anti-viral agent, cardiovascular agent, cholesterol-lowering agent,anti-diabetic agent, anti-allergic agent, pain-relieving agent, or acombination thereof. In certain embodiments, the compounds describedherein or pharmaceutical compositions can be administered in combinationwith an anti-cancer therapy including, but not limited to,transplantation (e.g., bone marrow transplantation, stem celltransplantation), surgery, radiation therapy, immunotherapy, andchemotherapy.

Also encompassed by the disclosure are kits (e.g., pharmaceuticalpacks). The kits provided may comprise a pharmaceutical composition orcompound described herein and a container (e.g., a vial, ampule, bottle,syringe, and/or dispenser package, or other suitable container). In someembodiments, provided kits may optionally further include a secondcontainer comprising a pharmaceutical excipient for dilution orsuspension of a pharmaceutical composition or compound described herein.In some embodiments, the pharmaceutical composition or compounddescribed herein provided in the first container and the secondcontainer are combined to form one unit dosage form.

Methods of Treatment and Uses

The present invention also provides methods for the treatment orprevention of a proliferative disease (e.g., cancers (e.g., leukemia,acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma,multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, braincancer, neuroblastoma, lung cancer, colorectal cancer), benignneoplasms, diseases associated with angiogenesis, inflammatory diseases,autoinflammatory diseases, and autoimmune diseases).

The compounds described herein may:

-   -   exhibit kinase inhibitory activity,    -   exhibit the ability to inhibit cyclin-dependent kinase (CDK),    -   exhibit the ability to inhibit cyclin-dependent kinase 7 (CDK7),    -   exhibit the ability to inhibit cyclin-dependent kinase 7 (CDK7),        without inhibiting another cyclin-dependent kinase (CDK),    -   exhibit a therapeutic effect and/or preventative effect in the        treatment of cancers,    -   exhibit a therapeutic effect and/or preventative effect in the        treatment of Myc-dependent cancers, and/or    -   exhibit a therapeutic profile (e.g., optimum safety and curative        effect) that is superior to existing chemotherapeutic agents.

Without wishing to be bound by any particular theory, the compoundsdescribed herein may be able to bind (e.g., covalently modify) a proteinkinase described herein. In certain embodiments, the R² group of acompound described herein may be able to bind (e.g., covalently modify)to the protein kinase. In certain embodiments, the R² group of acompound described herein may be able to covalently bind a cysteineresidue of the protein kinase. In certain embodiments, the R² group of acompound described herein may be able to covalently bind Cys312 residueof CDK7.

In another aspect, the present disclosure provides methods of inhibitingthe activity of a protein kinase in a subject, the methods comprisingadministering to the subject an effective amount (e.g., therapeuticallyeffective amount) of a compound, or pharmaceutical composition thereof,as described herein.

In another aspect, the present disclosure provides methods of inhibitingthe activity of a protein kinase in a biological sample, the methodscomprising contacting the biological sample with an effective amount ofa compound, or pharmaceutical composition thereof, as described herein.

In another aspect, the present disclosure provides methods of inhibitingthe activity of a protein kinase in a tissue, the methods comprisingcontacting the tissue with an effective amount of a compound, orpharmaceutical composition thereof, as described herein.

In another aspect, the present disclosure provides methods of inhibitingthe activity of a protein kinase in a cell, the methods comprisingcontacting the cell with an effective amount of a compound, orpharmaceutical composition thereof, as described herein.

In certain embodiments, the subject being treated is a mammal. Incertain embodiments, the subject is a human. In certain embodiments, thesubject is a domesticated animal, such as a dog, cat, cow, pig, horse,sheep, or goat. In certain embodiments, the subject is a companionanimal such as a dog or cat. In certain embodiments, the subject is alivestock animal such as a cow, pig, horse, sheep, or goat. In certainembodiments, the subject is a zoo animal. In another embodiment, thesubject is a research animal such as a rodent, dog, or non-humanprimate. In certain embodiments, the subject is a non-human transgenicanimal such as a transgenic mouse or transgenic pig.

In certain embodiments, a biological sample described herein is bonemarrow, lymph node, spleen, or blood.

In certain embodiments, a cell described herein is in vitro. In certainembodiments, a cell described herein is ex vivo. In certain embodiments,a cell described herein is in vivo. In certain embodiments, a celldescribed herein is a malignant cell (e.g., malignant blood cell). Incertain embodiments, a cell described herein is a malignanthematopoietic stem cell (e.g., malignant myeloid cell or malignantlymphoid cell). In certain embodiments, a cell described herein is amalignant lymphocyte (e.g., malignant T-cell or malignant B-cell). Incertain embodiments, a cell described herein is a malignant red bloodcell, malignant white blood cell, or malignant platelet. In certainembodiments, a cell described herein is a malignant neutrophil,malignant macrophage, or malignant plasma cell.

The proliferative disease to be treated or prevented using the compoundsdescribed herein may be associated with overexpression of a kinase, suchas cyclin-dependent kinase (CDK). The process of eukaryotic celldivision may be broadly divided into a series of sequential phasestermed G1, S, G2, and M. Correct progression through the various phasesof the cell cycle has been shown to be critically dependent upon thespatial and temporal regulation of a family of proteins known as cyclindependent kinases (CDKs) and a diverse set of their cognate proteinpartners termed cyclins. CDKs are CDC2 (also known as CDK1) homologousserine-threonine kinase proteins that are able to utilize ATP as asubstrate in the phosphorylation of diverse polypeptides in asequence-dependent context. Cyclins are a family of proteinscharacterized by a homology region, containing approximately 100 aminoacids, termed the “cyclin box” which is used in binding to, and definingselectivity for, specific CDK partner proteins.

Modulation of the expression levels, degradation rates, protein levels,and activity levels of various CDKs and cyclins throughout the cellcycle leads to the cyclical formation of a series of CDK/cyclincomplexes, in which the CDKs are enzymatically active. The formation ofthese complexes controls passage through discrete cell cycle checkpointsand thereby enables the process of cell division to continue. Failure tosatisfy the prerequisite biochemical criteria at a given cell cyclecheckpoint, i.e., failure to form a required CDK/cyclin complex, canlead to cell cycle arrest and/or cellular apoptosis. Aberrant cellularproliferation can often be attributed to loss of correct cell cyclecontrol. Inhibition of CDK enzymatic activity therefore provides a meansby which abnormally dividing cells can have their division arrestedand/or be killed. The diversity of CDKs, and CDK complexes, and theircritical roles in mediating the cell cycle, provides a broad spectrum ofpotential therapeutic targets selected on the basis of a definedbiochemical rationale.

CDK7, a member of the CDK family, was originally isolated as thecatalytic subunit of the trimeric CDK-activating kinase (CAK) complex.This complex, consisting of CDK7, cyclin H, and MAT 1, is responsiblefor activation of the mitotic promoting factor in vitro. The discoverythat CDK7 was also a component of the basal transcription repair factorIIH (TFIIH) implicated a dual role for CDK7 in transcription as part ofTFIIH and in the control of the cell cycle as the trimeric CAK complex.TFIIH is a multi-subunit protein complex identified as a factor requiredfor RNA polymerase II (RNAP II)-catalyzed transcription, andsubsequently this complex was found to play a key role in nucleotideexcision repair. CDK7 is a component of at least three complexes, i.e.,the trimeric CAK complex, the quaternary complex with the XPD (or ERCC2,a protein involved in transcription-coupled nucleotide excision repair),and the nine-subunit TFIIH complex. The two functions of CDK7 in CAK andCTD phosphorylation support critical facets of cellular proliferation,cell cycling, and transcription. Overexpression of CDK7 may inhibitapoptosis, promote transcription and cell proliferation, and/or disruptDNA repair, and therefore, cause proliferative diseases. In certainembodiments, the proliferative disease to be treated or prevented usingthe compounds described herein may be associated with overexpression ofa CDK (e.g., CDK7).

A proliferative disease may be associated with aberrant activity of aCDK (e.g., CDK7). Aberrant activity of a CDK (e.g., CDK7) may be anelevated and/or an inappropriate activity of the CDK. Deregulation ofcell cycle progression is a characteristic of a proliferative disease,and a majority of proliferative diseases have abnormalities in somecomponent of CDK (e.g., CDK7) activity, frequently through elevatedand/or inappropriate CDK activation. Inhibition of the catalyticactivity of CDK7 would be expected to inhibit cell cycle progression byblocking the phosphorylation of cell cycle CDKs, and would additionallyinhibit transcription of effectors of cell division. In certainembodiments, CDK7 is not overexpressed, and the activity of CDK7 iselevated and/or inappropriate. In certain other embodiments, CDK7 isoverexpressed, and the activity of CDK7 is elevated and/orinappropriate. The compounds described herein, and pharmaceuticallyacceptable salts, solvates, hydrates, polymorphs, co-crystals,tautomers, stereoisomers, isotopically labeled derivatives, prodrugs,and compositions thereof, may inhibit the activity of CDK7 and be usefulin treating and/or preventing proliferative diseases.

A proliferative disease may also be associated with inhibition ofapoptosis of a cell in a biological sample or subject. All types ofbiological samples described herein or known in the art are contemplatedas being within the scope of the invention. Apoptosis is the process ofprogrammed cell death. Inhibition of apoptosis may result inuncontrolled cell proliferation and, therefore, may cause proliferativediseases. The cell cycle CDKs (CDK1, 2, 4, and 6) are activated byphosphorylation by CDK7/cyclin H (also called CAK). Inhibition of CDK7would therefore result in cell-cycle arrest at multiple points in thecell cycle due to failure to activate the cell cycle CDKs. CDK 7activates transcription by phosphorylating the CTD of RNAP II.Inhibition of CTD phosphorylation has been shown to inhibittranscription and reduce expression of short lived proteins, includingthose involved in apoptosis regulation. It is appreciated in the artthat stalling of RNA polymerase may activate p53 (also known as protein53 or tumor protein 53, a tumor suppressor protein that is encoded inhumans by the TP53 gene), leading to apoptosis. Thus, inhibition of theactivity of CDK7 are expected to cause cytotoxicity by inducingapoptosis. The compounds described herein, and pharmaceuticallyacceptable salts, solvates, hydrates, polymorphs, co-crystals,tautomers, stereoisomers, isotopically labeled derivatives, prodrugs,and compositions thereof, may induce apoptosis, and therefore, be usefulin treating and/or preventing proliferative diseases.

In certain embodiments, the proliferative disease to be treated orprevented using the compounds described herein is cancer. All types ofcancers disclosed herein or known in the art are contemplated as beingwithin the scope of the invention. In certain embodiments, theproliferative disease is a cancer associated with dependence on BCL-2anti-apoptotic proteins (e.g., MCL-1 and/or XIAP). In certainembodiments, the proliferative disease is a cancer associated withoverexpression of MYC (a gene that codes for a transcription factor). Incertain embodiments, the cancer is a MYC-dependent cancer. In certainembodiments, the proliferative disease is a hematological malignancy. Incertain embodiments, the proliferative disease is a blood cancer. Incertain embodiments, the proliferative disease is a hematologicalmalignancy. In certain embodiments, the proliferative disease isleukemia. In certain embodiments, the proliferative disease is chroniclymphocytic leukemia (CLL). In certain embodiments, the proliferativedisease is acute lymphoblastic leukemia (ALL). In certain embodiments,the proliferative disease is T-cell acute lymphoblastic leukemia(T-ALL). In certain embodiments, the proliferative disease is chronicmyelogenous leukemia (CML). In certain embodiments, the proliferativedisease is acute myelogenous leukemia (AML). In certain embodiments, theproliferative disease is acute monocytic leukemia (AMoL). In certainembodiments, the proliferative disease is lymphoma. In some embodiments,the proliferative disease is Burkitt's lymphoma. In certain embodiments,the proliferative disease is a Hodgkin's lymphoma. In certainembodiments, the proliferative disease is a non-Hodgkin's lymphoma. Incertain embodiments, the proliferative disease is multiple myeloma. Incertain embodiments, the proliferative disease is melanoma. In certainembodiments, the proliferative disease is colorectal cancer. In certainembodiments, the proliferative disease is breast cancer. In certainembodiments, the proliferative disease is triple-negative breast cancer(TNBC). In certain embodiments, the proliferative disease is a bonecancer. In certain embodiments, the proliferative disease isosteosarcoma. In certain embodiments, the proliferative disease isEwing's sarcoma. In some embodiments, the proliferative disease is abrain cancer. In some embodiments, the proliferative disease isneuroblastoma. In some embodiments, the proliferative disease is a lungcancer. In some embodiments, the proliferative disease is small celllung cancer (SCLC). In some embodiments, the proliferative disease isnon-small cell lung cancer. In some embodiments, the proliferativedisease is a benign neoplasm. All types of benign neoplasms disclosedherein or known in the art are contemplated as being within the scope ofthe invention. In some embodiments, the proliferative disease isassociated with angiogenesis. All types of angiogenesis disclosed hereinor known in the art are contemplated as being within the scope of theinvention. In certain embodiments, the proliferative disease is aninflammatory disease. All types of inflammatory diseases disclosedherein or known in the art are contemplated as being within the scope ofthe invention. In certain embodiments, the inflammatory disease isrheumatoid arthritis. In some embodiments, the proliferative disease isan autoinflammatory disease. All types of autoinflammatory diseasesdisclosed herein or known in the art are contemplated as being withinthe scope of the invention. In some embodiments, the proliferativedisease is an autoimmune disease. All types of autoimmune diseasesdisclosed herein or known in the art are contemplated as being withinthe scope of the invention.

Another aspect of the invention relates to methods of inhibiting theactivity of a kinase in a biological sample or subject. In certainembodiments, the kinase is CDK. In certain embodiments, the kinase isCDK7. In certain embodiments, the activity of the kinase is aberrantactivity of the kinase. In certain embodiments, the inhibition of theactivity of the kinase is irreversible. In other embodiments, theinhibition of the activity of the kinase is reversible. In certainembodiments, the methods of inhibiting the activity of the kinaseinclude attaching a compound described herein to the kinase.

Also provided in the present invention are methods of inhibitingtranscription of genes in a biological sample or subject. Genes whichmay have their transcription inhibited by the compounds herein includeMYC, KLF2, E2F2, CDK6, CCND3, E2F3, HNRPDL, TET1, and IL7R.

The present invention also provides methods of inhibiting cell growth ina biological sample or subject.

In still another aspect, the present invention provides methods ofinducing apoptosis of a cell in a biological sample or a subject.

In certain embodiments, the methods described herein includeadministering to a subject or contacting a biological sample with aneffective amount of a compound described herein, or a pharmaceuticallyacceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer,stereoisomer, isotopically labeled derivative, or prodrug thereof, or apharmaceutical composition thereof. In certain embodiments, the methodsdescribed herein include administering to a subject or contacting abiological sample with an effective amount of a compound describedherein, or a pharmaceutically acceptable salt thereof, or apharmaceutical composition thereof. In certain embodiments, the compoundis contacted with a biological sample. In certain embodiments, thecompound is administered to a subject. In certain embodiments, thecompound is administered in combination with one or more additionalpharmaceutical agents described herein. The additional pharmaceuticalagent may be an anti-proliferative agent. In certain embodiments, theadditional pharmaceutical agent is an anti-cancer agent. The additionalpharmaceutical agent may also be a kinase inhibitor. In certainembodiments, the additional pharmaceutical agent is an inhibitor of aCDK. In certain embodiments, the additional pharmaceutical agent is aninhibitor of CDK7. In certain embodiments, the additional pharmaceuticalagent is a selective inhibitor of CDK7. In certain embodiments, theadditional pharmaceutical agent is a nonselective inhibitor of CDK7. Incertain embodiments, the additional pharmaceutical agent is an inhibitorof another CDK. In certain embodiments, the additional pharmaceuticalagent is a selective inhibitor of another CDK. In certain embodiments,the additional pharmaceutical agent is a nonselective inhibitor ofanother CDK. In certain embodiments, the additional pharmaceutical agentis flavopiridol, triptolide, SNS-032 (BMS-387032), PHA-767491,PHA-793887, BS-181, (S)-CR8, (R)-CR8, or NU6140. In certain embodiments,the additional pharmaceutical agent is an inhibitor of amitogen-activated protein kinase (MAPK). In certain embodiments, theadditional pharmaceutical agent is an inhibitor of a glycogen synthasekinase 3 (GSK3). In certain embodiments, the additional pharmaceuticalagent is an inhibitor of an AGC kinase. In certain embodiments, theadditional pharmaceutical agent is an inhibitor of acalmodulin-dependent kinase (CaM Kinase). In certain embodiments, theadditional pharmaceutical agent is an inhibitor of a casein kinase 1. Incertain embodiments, the additional pharmaceutical agent is an inhibitorof a STE kinase. In certain embodiments, the additional pharmaceuticalagent is an inhibitor of a tyrosine kinase.

In some embodiments, the additional pharmaceutical agent is atopoisomerase inhibitor, a MCL1 inhibitor, a BCL-2 inhibitor, a BCL-xLinhibitor, a BRD4 inhibitor, a CDK9 inhibitor, a Jumonji histonedemethylase inhibitor, or a DNA damage inducer. In some embodiments, theadditional pharmaceutical agent is etoposide, obatoclax, navitoclax,JQ1,4-(((5′-chloro-2′-(((1R,4R)-4-(((R)-1-methoxypropan-2-yl)amino)cyclohexyl)amino)-[2,4′-bipyridin]-6-yl)amino)methyl)tetrahydro-2H-pyran-4-carbonitrile,JIB04, or cisplatin. In some embodiments, the additional pharmaceuticalagent is etoposide, obatoclax, or navitoclax, and the disease to betreated is breast cancer, e.g., triple-negative breast cancer, HER2positive breast cancer, ER-positive breast cancer, or ER/PR-positivebreast cancer. In some embodiments, the additional pharmaceutical agentis etoposide, JIB04, or cisplatin, and the disease to be treated isEwing's sarcoma. In some embodiments, the additional pharmaceuticalagent is JQ1 or NVP2, and the disease to be treated is leukemia, e.g.,acute myelogenous leukemia, myeloblastic leukemia, promyelocyticleukemia, myelomonocytic leukemia, monocytic leukemia, monoblasticleukemia, or megakaryoblastic leukemia. In certain embodiments, apharmaceutical composition described herein further comprises acombination of the additional pharmaceutical agents described herein.

The inventive compounds or compositions may synergistically augmentinhibition of CDK7 induced by the additional pharmaceutical agent(s) inthe biological sample or subject. Thus, the combination of the inventivecompounds or compositions and the additional pharmaceutical agent(s) maybe useful in treating proliferative diseases resistant to a treatmentusing the additional pharmaceutical agent(s) without the inventivecompounds or compositions.

In some embodiments, the activity of a protein kinase is non-selectivelyinhibited by the compounds or pharmaceutical compositions describedherein. In some embodiments, the activity of a protein kinase describedherein is selectively inhibited by the compounds or pharmaceuticalcompositions described herein, compared to the activity of a differentprotein (e.g., a different protein kinase). In certain embodiments, theactivity of CDK (e.g., CDK7) is selectively inhibited by a compound orpharmaceutical composition described herein, compared to the activity ofa different protein. In certain embodiments, the activity of CDK7 isselectively inhibited by a compound or pharmaceutical compositiondescribed herein, compared to the activity of a different CDK protein.In certain embodiments, the activity of CDK7 is selectively inhibited bya compound or pharmaceutical composition described herein, compared tothe activity of CDK12. In certain embodiments, the activity of CDK7 isselectively inhibited by a compound or pharmaceutical compositiondescribed herein, compared to the activity of CDK13. In certainembodiments, the activity of CDK7 is selectively inhibited by a compoundor pharmaceutical composition described herein, compared to the activityof CDK12 and the activity of CDK13.

The selectivity of a compound or pharmaceutical composition describedherein in inhibiting the activity of a protein kinase over a differentprotein (e.g., a different protein kinase) may be measured by thequotient of the IC₅₀ value of the compound or pharmaceutical compositionin inhibiting the activity of the different protein over the IC₅₀ valueof the compound or pharmaceutical composition in inhibiting the activityof the protein kinase. The selectivity of a compound or pharmaceuticalcomposition described herein for a protein kinase over a differentprotein may also be measured by the quotient of the K_(d) value of anadduct of the compound or pharmaceutical composition and the differentprotein over the K_(d) value of an adduct of the compound orpharmaceutical composition and the protein kinase. In certainembodiments, the selectivity is at least 2-fold, at least 3-fold, atleast 5-fold, at least 10-fold, at least 30-fold, at least 100-fold, atleast 300-fold, at least 1,000-fold, at least 3,000-fold, at least10,000-fold, at least 30,000-fold, or at least 100,000-fold. In certainembodiments, the selectivity is not more than 100,000-fold, not morethan 10,000-fold, not more than 1,000-fold, not more than 100-fold, notmore than 10-fold, or not more than 2-fold. Combinations of theabove-referenced ranges (e.g., at least 2-fold and not more than10,000-fold) are also within the scope of the disclosure.

In certain embodiments, a kit described herein includes a firstcontainer comprising a compound or pharmaceutical composition describedherein. In certain embodiments, a kit described herein is useful intreating a proliferative disease (e.g., cancers (e.g., leukemia, acutelymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiplemyelomia, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer,neuroblastoma, lung cancer, colorectal cancer), benign neoplasms,diseases associated with angiogenesis, inflammatory diseases,autoinflammatory diseases, and autoimmune diseases) in a subject in needthereof, preventing a proliferative disease in a subject in needthereof, inhibiting the activity of a protein kinase (e.g., CDK (e.g.,CDK7)) in a subject, biological sample, tissue, or cell, and/or inducingapoptosis in a cell.

In certain embodiments, a kit described herein further includesinstructions for using the compound or pharmaceutical compositionincluded in the kit. A kit described herein may also include informationas required by a regulatory agency such as the U.S. Food and DrugAdministration (FDA). In certain embodiments, the information includedin the kits is prescribing information. In certain embodiments, the kitsand instructions provide for treating a proliferative disease in asubject in need thereof, preventing a proliferative disease in a subjectin need thereof, inhibiting the activity of a protein kinase (e.g., CDK(e.g., CDK7)) in a subject, biological sample, tissue, or cell, and/orinducing apoptosis in a cell. A kit described herein may include one ormore additional pharmaceutical agents described herein as a separatecomposition.

EXAMPLES

In order that the invention described herein may be more fullyunderstood, the following examples are set forth. The synthetic andbiological examples described in this application are offered toillustrate the compounds, pharmaceutical compositions, and methodsprovided herein and are not to be construed in any way as limiting theirscope.

Synthesis of the Compounds

The compounds provided herein can be prepared from readily availablestarting materials using the following general methods and procedures.Reactions were monitored by thin layer chromatography (TLC) with 0.25 mmE. Merck pre-coated silica gel plates (60 F₂₅₄) and Waters LCMS system(Waters 2489 UV/Visible Detector, Waters 3100 Mass, Waters 515 HPLCpump, Waters 2545 Binary Gradient Module, Waters Reagent Manager, Waters2767 Sample Manager) using SunFire™ C18 column (4.6×50 mm, 5 μm particlesize): solvent gradient=95% A at 0 min, 0% A at 5 min; solvent A=0.5%TFA in Water; solvent B=Methanol; flow rate: 1.5 mL/min. Purification ofreaction products was carried out by flash chromatography usingCombiFlash®Rf with Teledyne Isco RediSep®Rf High Performance Gold orSilicycle SiliaSep™ High Performance columns (4 g, 12 g, 24 g, 40 g, 80g or 120 g) or by Waters preparative HPLC system with a C18 column:solvent gradient—100% A at 0 min, 0% A at 15 min; solvent A—0.5% TFA inWater; solvent B=Methanol; flow rate: 20 mL/min. The purity of allcompounds was over 95% and was analyzed with Waters LCMS system. ¹H NMRand ¹³C NMR spectra were obtained using a Varian Inova-600 or 400 MHzspectrometer. Chemical shifts are reported relative to chloroform(δ=7.24) for ¹H NMR or dimethyl sulfoxide (δ=2.50) for ¹H NMR anddimethyl sulfoxide (δ=39.51) for ¹³C NMR. Data are reported as(br=broad, s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet).

Example 1.(S)-3-((3-(4-acrylamidobenzamido)phenyl)amino)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide(Compound 101)

The synthesis of Compound 101 follows Synthetic Scheme 1. The synthesesof Compounds 102 to 111 (presented in Table 2) follow a correspondingmethod.

5-(tert-Butyl) Ethyl3-amino-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate

To a solution of tert-butyl3-amino-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylate(1.0 g, 3.95 mmol) and TEA (0.6 g, 0.82 mL, 5.93 mmol) in THF (10 mL)was added ethyl chloroformate (0.43 g, 0.38 mL, 3.95 mmol) dropwise at0° C. The mixture was stirred at 0° C. for 1 h. The solvent wasevaporated and the residue was partitioned with EtOAc and sat. NaHCO₃.The organic layer was washed with water and brine, dried (Na₂SO₄). Thiswas concentrated to give 5-(tert-butyl) ethyl3-amino-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylateas an off white solid (1.28 g, 100%). LC/MS (ESI) m/z=325.3 (M+H)⁺.

5-(tert-Butyl) Ethyl6,6-dimethyl-3-((3-nitrophenyl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate

To a suspension of 5-(tert-butyl) ethyl3-amino-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(500 mg, 1.54 mmol), (3-nitrophenyl)boronic acid (514 mg, 3.08 mmol),and Cu(OAc)₂ (420 mg, 2.31 mmol) in DCM (10 mL) was added TEA (311 mg,0.43 mL, 3.08 mmol). The mixture was stirred at room temperatureovernight. Solvent was evaporated and the crude was purified by flashcolumn chromatography on silica gel (EtOAc/hexane, 0-70%) to give5-(tert-butyl) ethyl6,6-dimethyl-3-((3-nitrophenyl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylateas a yellow solid (240 mg, 35%). LC/MS (ESI) m/z=446.4 (M+H)⁺.

5-(tert-Butyl) Ethyl3-((3-aminophenyl)amino)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate

To a solution of 5-(tert-butyl) ethyl6,6-dimethyl-3-((3-nitrophenyl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(120 mg, 0.27 mmol) in EtOAc (2 mL) and pyridine (0.2 mL) was addedSnCl₂.2H₂O (305 mg, 1.35 mmol). The mixture was stirred at 70° C.overnight. The mixture was diluted with CHCl₃/i-PrOH (v/v 4:1) andwashed with sat. NaHCO₃ and brine, dried (Na₂SO₄), and concentrated. Thecrude was purified by flash column chromatography on silica gel(MeOH/DCM, 0-10%) to give 5-(tert-butyl) ethyl3-((3-aminophenyl)amino)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylateas a yellow solid (99 mg, 88%). LC/MS (ESI) m/z=416.4 (M+H)⁺.

5-(tert-Butyl) Ethyl6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate

To a solution of 5-(tert-butyl) ethyl3-((3-aminophenyl)amino)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(99 mg, 0.24 mmol) and DIEA (62 mg, 84 μL, 0.48 mmol) in DCM (2 mL) wasadded 4-nitrobenzoyl chloride (53 mg, 0.29 mmol) at 0° C. The reactionwas stirred at room temperature for 2 h and concentrated. The crude waspurified by flash column chromatography on silica gel (MeOH/DCM, 0-5%)to give 5-(tert-butyl) ethyl6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylateas a yellow solid (129 mg, 95%). LC/MS (ESI) m/z=565.4 (M+H)⁺.

Ethyl6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate

To a solution of 5-(tert-butyl) 1- or 2-ethyl6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(129 mg, 0.23 mmol) in DCM (1 mL) was added TFA (1 mL). The reaction wasstirred at room temperature for 1 h and concentrated to give ethyl6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylateas a TFA salt, which was used directly without further purification.LC/MS (ESI) m/z=464.4 (M+H)⁻.

Ethyl(S)-5-((2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate

To a mixture of ethyl6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate(TFA salt, 0.23 mmol) in DCM (2 mL) was added DIEA (148 mg, 0.2 mL, 1.15mmol) at 0° C., followed by(S)-2-isocyanato-N,N-dimethyl-2-phenylethan-1-amine HCl salt (62 mg,0.27 mmol). The solution was stirred at 0° C. for 1 h and diluted withCHCl₃/i-PrOH (v/v 4:1) and washed with sat. NaHCO₃ and brine, dried(Na₂SO₄), and concentrated. The crude was purified by flash columnchromatography on silica gel (1.75 M NH₃ in MeOH/DCM, 0-10%) to giveethyl(S)-5-((2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylateas a yellow solid (134 mg, 89% over 2 steps). LC/MS (ESI) m/z=655.4(M+H)⁺.

Ethyl(S)-3-((3-(4-aminobenzamido)phenyl)amino)-5-((2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate

To a solution of ethyl(S)-5-((2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-3-((3-(4-nitrobenzamido)phenyl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate(134 mg, 0.20 mmol) in EtOAc (2 mL) was added SnCl₂.2H₂O (226 mg, 1.0mmol). The mixture was stirred at 70° C. for 2 h and diluted withCHCl₃/i-PrOH (v/v 4:1) and washed with sat. NaHCO₃ and brine, dried(Na₂SO₄), and concentrated. The crude was purified by flash columnchromatography on silica gel (1.75 M NH₃ in MeOH/DCM, 0-10%) to giveethyl(S)-3-((3-(4-aminobenzamido)phenyl)amino)-5-((2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylateas a yellow solid (112 mg, 90%). LC/MS (ESI) m/z=625.4 (M+H)⁺.

Compound 101.(S)-3-((3-(4-acrylamidobenzamido)phenyl)amino)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

To a mixture of ethyl(S)-3-((3-(4-aminobenzamido)phenyl)amino)-5-((2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate(20 mg, 0.032 mmol) in THF (1 mL) and sat. NaHCO₃ (1 mL) was addedacryloyl chloride (5.8 mg, 0.064 mmol) dropwise at 0° C. The mixture wasstirred at 0° C. for 10 min and diluted with CHCl₃/i-PrOH (v/v 4:1) andwashed with sat. NaHCO₃ and brine, dried (Na₂SO₄), and concentrated. Thecrude ethyl(S)-3-((3-(4-acrylamidobenzamido)phenyl)amino)-5-((2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate was dissolved in i-PrOH (1 mL) and LiOH (1 M, 1 mL) wasadded. After stirred at room temperature for 10 min, the mixture wasdiluted with CHCl₃/i-PrOH (v/v 4:1) and washed with sat. NaHCO₃ andbrine, dried (Na₂SO₄), and concentrated. The crude was purified byreverse phase preparative HPLC (MeOH/H₂O, 0-100%) to give(S)-3-((3-(4-acrylamidobenzamido)phenyl)amino)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamideas a white solid (10.5 mg, 54%). ¹H NMR: 600 MHz (DMSO-d₆) δ 10.44 (d,J=4.2 Hz, 1H), 10.04 (s, 1H), 8.33 (s, 1H), 7.96-7.93 (m, 2H), 7.82-7.80(m, 2H), 7.34-7.32 (m, 2H), 7.26-7.23 (m, 2H), 7.20-7.10 (m, 3H),6.52-6.46 (m, 1H), 6.35-6.30 (m, 1H), 6.09 (s, 1H), 5.84-5.81 (m, 1H),4.89-4.83 (m, 1H), 4.35 (d, J=19.8 Hz, 2H), 2.64-2.57 (m, 1H), 2.45-2.38(m, 1H), 2.18 (s, 6H), 1.65 (d, J=4.2 Hz, 3H), 1.58 (d, J=4.8 Hz, 3H);MS m/z: 607.4 [M+1].

TABLE 2 The following compounds were produced by using the correspondingstarting compounds according to a method similar to that described inExample 1: Name Structure Characterization Data Compound 102(S)-3-((4-(4- acrylamidobenzamido) phenyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.46 (s, 1H), 10.01 (s, 1H),8.98-8.89 (br, 1H), 8.25 (s, 1H), 7.99 (d, J = 8.8 Hz, 2H), 7.85 (d, J =8.8 Hz, 2H), 7.64 (d, J = 8.8 Hz, 2H), 7.48-7.42 (m, 4H), 7.38- 7.34 (m,1H), 7.00-6.91 (m, 2H), 6.69 (d, J = 8.8 Hz, 1H), 6.53 (dd, J = 17.2,10.0 Hz, 1H), 6.36 (dd, J = 17.2, 2.0 Hz, 1H), 5.87 (dd, J = 10.0, 2.0Hz, 1H), 5.40-5.35 (m, 1H), 4.48 (d, J = 10.8 Hz, 1H), 4.33 (d, J = 10.8Hz, 1H), 3.10-2.95 (m, 2H), 2.93 (d, J = 4.8 Hz, 3H), 2.87 (d, J = 4.8Hz, 3H), 1.74 (s, 3H), 1.65 (s, 3H); MS m/z: 607.4 [M + 1]. Compound 103(S)-3-((4-(3- acrylamidobenzamido) phenyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 11.90-11.70 (br, 1H), 10.26 (s,1H), 9.98 (s, 1H), 8.22-8.10 (br, 1H), 8.07 (m, 1H), 7.83 (dd, J = 8.0,1.2 Hz, 1H), 7.57 (d, J = 8.0 Hz, 1H), 7.51 (d, J = 8.8 Hz, 2H), 7.39(t, J = 8.0 Hz, 1H), 7.27 (d, J = 7.2 Hz, 2H), 7.22 (t, J = 7.2 Hz, 2H),7.12 (t, J = 7.2 Hz, 1H), 6.39 (dd, J = 17.2, 10.0 Hz, 1H), 6.22 (dd, J= 17.2, 2.0 Hz, 1H), 6.03-5.92 (m, 1H), 5.72 (dd, J = 10.0, 2.0 Hz, 1H),4.60-4.51 (m, 1H), 4.25-4.14 (m, 2H), 2.52 (dd, J = 12.0, 8.8 Hz, 1H),2.32-2.27 (m, 1H), 2.10 (s, 6H), 1.57 (s, 3H), 1.50 (s, 3H); MS m/z:607.4 [M + 1]. Compound 104 (S)-N-(2-(dimethylamino)-1-phenylethyl)-6,6- dimethyl-3-((3-(4- propionamidobenzamido)phenyl)amino)-4,6- dihydropyrrolo[3,4- c]pyrazole-5(1H)- carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 12.20-11.80 (br, 1H), 10.09 (s,1H), 9.93 (s, 1H), 8.23 (s, 1H), 7.83 (d, J = 8.0 Hz, 2H), 7.65 (d, J =8.8 Hz, 2H), 7.50-7.30 (m, 1H), 7.27 (d, J = 6.8 Hz, 2H), 7.18 (t, J =7.2 Hz, 2H), 7.13-7.09 (m, 3H), 6.59-6.51 (m, 1H), 6.12 (s, 1H),4.92-4.80 (m, 1H), 4.29 (s, 2H), 2.30 (q, J = 7.6 Hz, 2H), 2.22 (m, 6H),1.57 (s, 3H), 1.51 (s, 3H), 1.03 (t, J = 7.6 Hz, 3H); MS m/z: 609.4 [M +1]. Compound 105 (S)-3-((3-(3- acrylamidobenzamido) phenyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo(3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 12.10-11.82 (br, 1H), 10.26 (s,1H), 10.08 (s, 1H), 8.25 (s, 1H), 8.06 (s, 1H), 7.85 (dd, J = 8.4, 1.2Hz, 1H), 7.55 (d, J = 7.6 Hz, 1H), 7.39 (t, J = 8.0 Hz, 1H), 7.24 (d, J= 7.2 Hz, 2H), 7.15 (t, J = 7.2 Hz, 2H), 7.08 (d, J = 6.4 Hz, 1H), 6.39(dd, J = 17.2, 10.0 Hz, 1H), 6.22 (dd, J = 17.2, 2.0 Hz, 1H), 5.97 (s,1H), 5.72 (dd, J = 10.0, 2.0 Hz, 1H), 4.76- 4.70 (m, 1H), 4.30-4.19 (m,2H), 2.50-2.44 (m, 1H), 2.29- 2.22 (m, 1H), 2.05 (s, 6H), 1.57 (s, 3H),1.50 (s, 3H); MS m/z: 607.4 [M +1]. Compound 106 3-((3-(4-acrylamidobenzamido) phenyl)amino)-N-(2- (dimethylamino)ethyl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4- c]pyrazole-5(1H)- carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.49 (s, 1H), 10.07 (s, 1H),9.41 (s, 1H), 8.37 (s, 1H), 7.99 (d, J = 8.8 Hz, 2H), 7.86 (d, J = 8.8Hz, 2H), 7.49 (s, 1H), 7.21 (m, 2H), 6.74 (m, 1H), 6.53 (dd, J = 17.2,10.0 Hz, 1H), 6.38 (m, 1H), 6.36 (dd, J = 17.2, 2.0 Hz, 1H), 5.87 (dd, J= 10.0, 2.0 Hz, 1H), 4.27 (s, 2H), 3.41 (q, J = 5.6 Hz, 2H), 3.18 (q, J= 5.6 Hz, 2H), 2.86 (s, 3H), 2.85 (s, 3H), 1.71 (s, 6H); MS m/z: 531.4[M + 1]. Compound 107 4-acrylamido-N-(3-((6,6- dimethyl-5-(4-methylpiperazine-1- carbonyl)-1,4,5,6- tetrahydropyrrolo[3,4-c]pyrazol-3- yl)amino)phenyl)benzamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.49 (s, 1H), 10.08 (s, 1H),9.68 (s, 1H), 8.44 (s, 1H), 7.99 (d, J = 8.8 Hz, 2H), 7.86 (d, J = 8.4Hz, 2H), 7.62 (s, 1H), 7.23-7.13 (m, 2H), 6.84 (d, J = 12 Hz, 1H), 6.53(dd, J = 17.2, 10.0 Hz, 1H), 6.36 (dd, J = 17.2, 2.0 Hz, 1H), 5.87 (dd,J = 10.0, 2.0 Hz, 1H), 4.43 (s, 2H), 3.40- 3.33 (m, 4H), 3.15-2.97 (m,4H), 2.82 (s, 3H), 1.70 (s, 6H); MS m/z: 543.4 [M + 1]. Compound 1083-((3-(4- acrylamidobenzamido) phenyl)amino)-N-(1-(dimethylamino)propan-2- yl)-6,6-dimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.35 (s, 1H), 9.95 (s, 1H), 8.91(s, 1H), 8.23 (s, 1H), 7.85 (d, J = 8.4 Hz, 2H), 7.72 (d, J = 8.4 Hz,2H), 7.32 (s, 1H), 7.11-7.05 (m, 2H), 6.57 (m, 1H), 6.40 (dd, J = 16.8,10.0 Hz, 1H), 6.23 (dd, J = 16.8, 2.0 Hz, 1H), 5.91 (d, J = 8.4 Hz, 1H),5.74 (dd, J = 10.0, 2.0 Hz, 1H), 4.18 (s, 2H), 4.14-4.07 (m, 1H),3.05-2.94 (m, 2H), 2.71 (d, J = 4.8 Hz, 3H), 2.69 (d, J = 4.8 Hz, 3H),1.59 (s, 6H), 1.01 (d, J = 6.4 Hz, 3H), 0.85-0.76 (m, 1H); MS m/z: 545.3[M + 1]. Compound 109 (S,E)-3-((3-(4-(4- (dimethylamino)but-2-enamido)benzamido)phenyl) amino)-N-(2-hydroxy-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.68 (s, 1H), 10.13 (s, 1H),10.01 (s, 1H), 8.43 (s, 1H), 8.03 (d, J = 8.8 Hz, 2H), 7.88 (d, J = 8.8Hz, 2H), 7.54 (s, 1H), 7.41-7.39 (m, 2H), 7.34-7.30 (m, 2H), 7.27-7.22(m, 3H), 6.92-6.82 (m, 2H), 6.58 (d, J = 15.6 Hz, 1H), 6.13 (d, J = 8.0Hz, 1H), 4.85 (q, J = 6.8 Hz, 1H), 4.48 (q, J = 11.2 Hz, 2H), 4.06 (d, J= 7.2 Hz, 2H), 3.63 (d, J = 6.4 Hz, 2H), 2.91 (s, 6H), 2.64 (t, J = 5.6Hz, 1H), 1.73 (s, 3H), 1.67 (s, 3H); MS m/z: 637.3 [M + 1]. Compound 110(S)-3-((3- acrylamidophenyl)amino)- N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 9.94 (s, 1H), 8.90 (s, 1H), 8.24(s, 1H), 7.35-7.27 (m, 4H), 7.24-7.22 (m, 2H), 7.08-7.02 (m, 2H),6.56-6.52 (m, 2H), 6.38 (dd, J = 16.8, 10.0 Hz, 1H), 6.16 (dd, J = 16.8,2.0 Hz, 1H), 5.67 (dd, 10.0, 2.0 Hz, 1H), 5.29-5.22 (m, 1H), 4.31 (q, J= 11.2 Hz, 2H), 3.39-3.34 (m, 1H), 3.28- 3.22 (m, 1H), 2.80 (d, J = 4.8Hz, 1H), 2.73 (d, J = 4.8 Hz, 1H), 1.59 (s, 3H), 1.53 (s, 3H); MS m/z:488.3 [M + 1]. Compound 111 (S)-3-((4- acrylamidophenyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4- c)pyrazole-5(1H)- carboxamide

¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 9.86 (s, 1H), 8.91 (s, 1H), 8.13(s, 1H), 7.49-7.43 (m, 2H), 7.40-7.27 (m, 5H), 7.22 (m, 1H), 6.82 (d, J= 9.2 Hz, 1H), 6.55 (d, J = 9.2 Hz, 1H), 6.34 (dd, J = 16.8, 10.0 Hz,1H), 6.13 (dd, J = 16.8, 2.0 Hz, 1H), 5.62 (dd, J = 10.0, 2.0 Hz, 1H),5.29-5.22 (m, 1H), 4.33 (d, J = 11.2 Hz, 1H), 4.19 (d, J = 11.2 Hz, 1H),3.42-3.36 (m, 1H), 3.29-3.23 (m, 1H), 2.81 (d, J = 4.8 Hz, 1H), 2.74 (d,J = 4.8 Hz, 1H), 1.60 (s, 3H), 1.51 (s, 3H); MS m/z: 488.3 [M + 1].

Example 2.(S)-3-(3-(4-acrylamidobenzamido)benzamido)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide(Compound 112)

The synthesis of Compound 112 follows Synthetic Scheme 2. The synthesesof Compounds 120, and 214 to 217 (presented in Table 3) follow acorresponding method.

5-(tert-Butyl) Ethyl6,6-dimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate

To a solution of 5-(tert-butyl) ethyl3-amino-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(100 mg, 0.31 mmol) and DIEA (79 mg, 0.11 mL, 0.62 mmol) in DCM (2 mL)was added 3-nitrobenzoyl chloride (87 mg, 0.47 mmol). The reaction wasstirred at room temperature for 2 h and concentrated. The crude waspurified by flash column chromatography on silica gel (EtOAc/hexanes,0-70%) to give 5-(tert-Butyl) ethyl6,6-dimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylateas a yellow solid (110 mg, 75%). LC/MS (ESI) m/z=474.4 (M+H)⁺.

Compound 112.(S)-3-(3-(4-acrylamidobenzamido)benzamido)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

Following the previously described synthetic procedure of Compound 101from 5-(tert-butyl) ethyl6,6-dimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate,(S)-3-(3-(4-acrylamidobenzamido)benzamido)-N-(2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamidewas obtained as a white solid. ¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ10.97 (s, 1H), 10.53 (s, 1H), 10.40 (s, 1H), 9.04 (s, 1H), 8.62 (m, 1H),8.04 (d, J=9.2 Hz, 2H), 7.89 (d, J=9.2 Hz, 2H), 7.83 (d, J=7.6 Hz, 1H),7.57-7.44 (m, 4H), 7.36 (t, J=7.2 Hz, 1H), 6.83 (d, J=9.2 Hz, 1H), 6.54(dd, J=17.2, 10.0 Hz, 1H), 6.37 (dd, J=17.2, 2.0 Hz, 1H), 5.88 (dd,J=10.0, 2.0 Hz, 1H), 5.43-5.37 (m, 1H), 4.86 (d, J=12.4 Hz, 1H), 4.64(d, J=11.6 Hz, 1H), 2.95 (d, J=8.4 Hz, 3H), 2.90 (d, J=8.4 Hz, 3H), 1.74(s, 3H), 1.66 (s, 3H); MS m/z: 635.3 [M+1].

TABLE 3 The following compounds were produced using the correspondingstarting compounds according to a method similar to that described forsynthesis of Compound 112: Name Structure Characterization Data Compound120. (S)-3-(3- acrylamidobenzamido)-N- (2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR (TFA salt): 600 MHz (DMSO-d₆) δ 10.77 (s, 1H), 10.19 (s, 1H),8.86 (s, 1H), 8.32 (s, 1H), 7.60 (m, 1H), 7.54 (m, 1H), 7.28 (m, 4H),7.15 (m, 1H), 6.62 (m, 1H), 6.31 (m, 1H), 6.14 (m, 1H), 5.64 (m, 1H),5.19 (m, 1H), 4.64 (m, 1H), 4.42 (m, 1H), 3.41 (m, 1H), 3.19 (m, 1H),2.73 (m, 3H), 2.69 (m, 3H), 1.53 (s, 3H), 1.44 (s, 3H); MS m/z: 516.3[M + 1]. Compound 214. (S)-3-(4- acrylamidobenzamido)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 10.80 (s, 1H), 10.43 (s, 1H), 8.98 (s, 1H),7.99 (d, J = 8.8 Hz, 2H), 7.78 (d, J = 8.8 Hz, 2H), 7.71 (d, J = 7.6 Hz,2H), 7.38 (t, J = 7.0 Hz, 2H), 7.28 (t, J = 7.0 Hz, 1H), 6.75 (d, J =9.4 Hz, 1H), 6.45 (dd, J = 17.0, 10.0 Hz, 1H), 6.29 (dd, J = 16.4, 2.4Hz, 1H), 5.80 (dd, J = 10.0, 1.8 Hz, 1H), 5.33 (m, 1H), 4.75 (d, J =11.7 Hz, 1H), 4.53 (d, J = 11.7 Hz, 1H), 3.53 (m, 1H), 3.33 (m, 1H),2.86 (d, J = 4.7 Hz, 3H), 2.82 (d, J = 5.3 Hz, 3H), 1.65 (s, 3H), 1.57(s, 3H); MS m/z: 516.3 [M + 1]. Compound 215. (S)-N-(2-(dimethylamino)-1-phenylethyl)-6,6- dimethyl-3-(4- propionamidobenzamido)-4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)- carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 12.38 (s, 1H), 10.71 (s, 1H), 10.12 (s,1H), 7.95 (m, 2H), 7.69 (m, 2H), 7.35 (d, J = 7.0 Hz, 2H), 7.28 (t, J =7.6 Hz, 2H), 7.18 (d, J = 7.6 Hz, 1H), 6.25 (m, 1H), 4.87 (m, 1H), 4.52(m, 2H), 2.68 (m, 1H), 2.41 (m, 1H), 2.34 (q, J = 7.6 Hz, 2H), 2.20 (m,6H), 1.62 (m, 3H), 1.55 (s, 3H), 1.08 (t, J = 7.6 Hz, 1H); MS m/z: 518.3[M + 1]. Compound 216. (S)-3-(4-acrylamido-2- methoxybenzamido)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR (a mixture of rotamers): 600 MHz (DMSO- d₆) δ 12.41, 12.32 (s,1H), 10.49, 10.45 (s, 1H), 10.29, 10.09 (s, 1H), 8.97 (br, 1H), 7.86 (m,1H), 7.63 (m, 1H), 7.38 (m, 2H), 7.32 (m, 2H), 7.22 (m, 1H), 6.44 (dd, J= 17.0, 10.0 Hz, 1H), 6.30 (dd, J = 17.0, 1.2 Hz, 1H), 5.81 (d, J = 11.7Hz, 1H), 5.05 (br, 1H), 4.63 (m, 1H), 4.57 (m, 1H), 3.95 (m, 3H),2.70-2.20 (m, 6H), 1.64, 1.60 (s, 3H), 1.56, 1.52 (s, 3H); MS m/z: 546.3[M + 1]. Compound 217. (S)-3-(4-acrylamido-3- methoxybenzamido)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 12.44 (s, 1H), 10.87 (s, 1H), 9.55 (s, 1H),8.26 (m, 1H), 7.72 (s, 1H), 7.65 (m, 1H), 7.38 (m, 2H), 7.32 (m, 2H),7.23 (m, 1H), 6.76 (dd, J = 17.0, 10.0 Hz, 1H), 6.46 (br, 1H), 6.25 (dd,J = 17.0, 1.8 Hz, 1H), 5.75 (d, J = 10.0 Hz, 1H), 5.07 (br, 1H), 4.63(m, 1H), 4.56 (m, 1H), 3.94 (s, 3H), 2.79-2.06 (m, 6H), 1.64 (s, 3H),1.57 (s, 3H); MS m/z: 546.3 [M + 1].

Example 3.3-(1-acryloylpiperidine-3-carboxamido)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide(Compounds 113 & 114)

The synthesis of Compounds 113 follows Synthetic Scheme 3. The synthesisof Compounds 114, 123, 221, and 222 (presented in Table 4) follows acorresponding method.

5-(tert-Butyl) Ethyl(R)-3-(1-((benzyloxy)carbonyl)piperidine-3-carboxamido)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate

To a solution of 5-(tert-butyl) ethyl3-amino-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(100 mg, 0.31 mmol), (R)-1-((benzyloxy)carbonyl)piperidine-3-carboxylicacid (122 mg, 0.47 mmol), and DIEA (120 mg, 0.16 mL, 0.93 mmol) in DMF(2 mL) was HATU (236 mg, 0.62 mmol). The mixture was stirred at roomtemperature overnight and diluted with ethyl acetate and sat. NaHCO₃.The organic layer was washed with water and brine, dried (Na₂SO₄), andconcentrated. The crude was purified by flash column chromatography onsilica gel (EtOAc/hexanes, 0-70%) to give 5-(tert-butyl) ethyl(R)-3-(1-((benzyloxy)carbonyl)piperidine-3-carboxamido)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylateas a yellow solid (65 mg, 37%). LC/MS (ESI) m/z=570.4 (M+H)⁺.

Ethyl3-((R)-1-((benzyloxy)carbonyl)piperidine-3-carboxamido)-5-(((S)-2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate

To a solution of 5-(tert-butyl) ethyl(R)-3-(1-((benzyloxy)carbonyl)piperidine-3-carboxamido)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(65 mg, 0.115 mmol) in DCM (1 mL) was added TFA (1 mL). The reaction wasstirred at room temperature for 1 h and concentrated to give ethyl(R)-3-(1-((benzyloxy)carbonyl)piperidine-3-carboxamido)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate as a TFA salt, which was used directly without furtherpurification. LC/MS (ESI) m/z=470.4 (M+H)⁺.

To a mixture of(R)-3-(1-((benzyloxy)carbonyl)piperidine-3-carboxamido)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate (TFA salt, 0.115 mmol) in DCM (1 mL) was added DIEA (74mg, 0.1 mL, 0.57 mmol) at 0° C., followed by(S)-2-isocyanato-N,N-dimethyl-2-phenylethan-1-amine HCl salt (31 mg,0.14 mmol). The solution was stirred at 0° C. for 1 h and diluted withCHCl₃/i-PrOH (v/v 4:1) and washed with sat. NaHCO₃ and brine, dried(Na₂SO₄), and concentrated. The crude was purified by flash columnchromatography on silica gel (1.75 M NH₃ in MeOH/DCM, 0-10%) to giveethyl3-((R)-1-((benzyloxy)carbonyl)piperidine-3-carboxamido)-5-(((S)-2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate as a yellow solid (53 mg, 70% over 2 steps). LC/MS(ESI) m/z=660.4 (M+H)⁺.

N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-3-((R)-piperidine-3-carboxamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

A mixture of ethyl3-((R)-1-((benzyloxy)carbonyl)piperidine-3-carboxamido)-5-(((S)-2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate(53 mg, 0.081 mmol) and 10% Pd/C (10 mg) in MeOH (5 mL) was degassed.The mixture was stirred under H₂ (1 atm) at room temperature overnight.The reaction was filtered through Celite® and concentrated to giveN—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-3-((R)-piperidine-3-carboxamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamideas a clear wax (28 mg, 78%). LC/MS (ESI) m/z: 454.4 (M+H)⁺.

Compound 113:3-((R)-1-acryloylpiperidine-3-carboxamido)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

To a mixture ofN—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-3-((R)-piperidine-3-carboxamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide(20 mg, 0.044 mmol) in THF (1 mL) and sat. NaHCO₃ (1 mL) was addedacryloyl chloride (12 mg, 0.13 mmol) dropwise at 0° C. The mixture wasstirred at 0° C. for 10 min and diluted with CHCl₃/i-PrOH (v/v 4:1) andwashed with sat. NaHCO₃ and brine, dried (Na₂SO₄), and concentrated. Thecrude was dissolved in i-PrOH (1 mL) and LiOH (1 M, 1 mL) was added.After stirred at room temperature for 10 min, the mixture was dilutedwith CHCl₃/i-PrOH (v/v 4:1) and washed with sat. NaHCO₃ and brine, dried(Na₂SO₄), and concentrated. The crude was purified by reverse phasepreparative HPLC (MeOH/H₂O, 0-100%) to give3-((R)-1-acryloylpiperidine-3-carboxamido)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamideTFA salt as a white solid (11 mg, 42%). ¹H NMR (TFA salt): 600 MHz(DMSO-d₆) δ 10.56 (d, J=19.8 Hz, 1H), 8.95 (s, 1H), 7.41-7.36 (m, 3H),7.31-7.27 (m, 1H), 6.87-6.79 (m, 1H), 6.72 (d, J=9.0 Hz, 1H), 6.08 (d,J=16.2 Hz, 1H), 5.66 (d, J=10.2 Hz, 1H), 5.32 (m, 1H), 4.69 (m, 1H),4.47 (m, 2H), 4.03 (m, 2H), 3.53 (t, J=12.0 Hz, 2H), 3.35-3.30 (m, 1H),3.18-3.12 (m, 1H), 2.99 (t, J=13.2 Hz, 1H), 2.85 (d, J=5.4 Hz, 3H), 2.82(d, J=4.8 Hz, 3H), 2.70 (t, J=12.0 Hz, 1H), 1.95 (m, 1H), 1.73 (m, 1H),1.62 (s, 3H), 1.53 (s, 3H), 1.33 (m, 1H); MS m/z: 508.3 [M+1].

Compound 114.3-((S)-1-acryloylpiperidine-3-carboxamido)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

3-((S)-1-Acryloylpiperidine-3-carboxamido)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide was prepared by using the corresponding startingcompounds according to a method similar to that described for Compound113. ¹H NMR (TFA salt): 400 MHz (DMSO-d₆) δ 10.50 (d, J=15.6 Hz, 1H),8.90 (s, 1H), 7.37-7.31 (m, 4H), 7.25-7.21 (m, 1H), 6.82-6.72 (m, 1H),6.66 (d, J=8.8 Hz, 1H), 6.03 (d, J=16.4 Hz, 1H), 5.61 (d, J=10.8 Hz,1H), 5.27 (m, 1H), 4.62 (m, 1H), 4.43 (m, 2H), 4.07-3.96 (m, 2H),3.13-3.05 (m, 2H), 2.94 (t, J=12.0 Hz, 1H), 2.81 (d, J=5.2 Hz, 3H), 2.77(d, J=5.2 Hz, 3H), 2.69-2.57 (m, 1H), 1.89 (m, 1H), 1.67 (m, 1H), 1.57(s, 3H), 1.49 (s, 3H), 1.29 (m, 1H); MS m/z: 508.3 [M+1].

TABLE 4 The following compounds were produced using the correspondingstarting compounds according to a method similar to that described forthe synthesis of Compound 113: Name Structure Characterization DataCompound 123 (S)-3-(1-acryloylpiperidine- 4-carboxamido)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR (TFA salt): 600 MHz (DMSO-d₆) δ 10.45 (s, 1H), 8.93 (s, 1H), 7.35(m, 3H), 7.25 (t, J = 7.0 Hz, 1H), 6.76 (dd, J = 16.4, 10.6 Hz, 1H),6.67 (d, J = 9.4 Hz, 1H), 6.04 (dd, J = 16.4, 2.4 Hz, 1H), 5.62 (dd, J =10.6, 2.4 Hz, 1H), 5.28 (td, J = 12.3, 3.5 Hz, 1H), 4.64 (d, J = 11.7Hz, 1H), 4.43 (d, J = 12.3 Hz, 1H), 4.39 (d, J = 12.3 Hz, 1H), 4.05 (d,J = 14.1 Hz, 1H), 3.49 (t, J = 12.3 Hz, 1H), 3.29 (m, 1H), 3.04 (t, J =12.9 Hz, 1H), 2.81 (d, J = 4.7 Hz, 3H), 2.79 (d, J = 4.7 Hz, 3H), 2.82(m, 2H), 1.77 (m, 2H), 1.58 (s, 3H), 1.50 (s, 3H), 1.42 (m, 2H); MS m/z:508.3 [M + 1]. Compound 221. 3-((1s,4R)-4- acrylamidocyclohexane-1-carboxamido)-N-((S)-2- (dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo(3,4- c]pyrazole-5(1H)- carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 12.26 (s, 1H), 10.27 (s, 1H), 7.92 (s, 1H),7.37 (m, 2H), 7.32 (m, 2H), 7.23 (m, 1H), 6.32 (dd, J = 17.0, 10.6 Hz,1H), 6.06 (dd, J = 17.0, 2.4 Hz, 1H), 5.54 (dd, J = 10.0, 2.4 Hz, 1H),4.56 (m, 1H), 4.48 (m, 1H), 3.86 (m, 1H), 2.43 (m, 2H), 1.76 (m, 4H),1.60 (s, 3H), 1.57 (m, 2H), 1.53 (s, 3H); MS m/z: 522.3 [M + 1].Compound 222 3-((1r,4S)-4- acrylamidocyclohexane-1-carboxamido)-N-((S)-2- (dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)- carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 12.24 (s, 1H), 10.31 (s, 1H), 7.97 (d, J =7.6 Hz, 1H), 7.36 (d, J = 7.0 Hz, 2H), 7.29 (t, J = 7.6 Hz, 2H), 7.20(t, J = 7.6 Hz, 1H), 6.34 (m, 1H), 6.16 (dd, J = 17.2, 10.0 Hz, 1H),6.05 (dd, J = 17.0, 2.4 Hz, 1H), 5.55 (dd, J = 10.0, 2.4 Hz, 1H), 4.94(m, 1H), 4.48 (m, 2H), 3.55 (m, 1H), 2.32 (m, 6H), 1.84 (m, 4H), 1.59(s, 3H), 1.51 (s, 3H), 1.48 (m, 2H), 1.21 (m, 2H); MS m/z: 522.3 [M +1].

Example 4.3-((1-(4-acrylamidobenzoyl)piperidin-3-yl)amino)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide(Compound 115)

The synthesis of Compounds 115 follows Synthetic Scheme 4. The synthesesof Compounds 116 to 119, and Compounds 228 to 232 (presented in Table 5)follow a corresponding method.

Tert-Butyl6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylate

To a solution of tert-butyl3-amino-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylate(50 mg, 0.20 mmol) in THF (1 mL) was added1-(4-nitrobenzoyl)piperidin-3-one (49 mg, 0.20 mmol), followed by AcOH(5 drops) and Na(OAc)₃BH (127 mg, 0.60 mmol). The mixture was stirred atroom temperature O/N and diluted with EtOAc and sat. NaHCO₃. The organiclayer was washed with water and brine, dried (Na₂SO₄), and concentrated.The crude was purified by reverse phase preparative HPLC (MeOH/H₂O,0-100%) to give tert-butyl6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylateas a TFA salt (48 mg, 40%). LC/MS (ESI) m/z: 485.4 (M+H)⁺.

1-Benzyl 5-(tert-butyl)6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate

To a solution of tert-butyl6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylateTFA salt (48 mg, 0.08 mmol) in THF (2 mL) was added DIEA (31 mg, 42 μL,0.24 mmol) at 0° C. Benzyl chloroformate (14 mg, 0.08 mmol) was addeddropwise and stirred at 0° C. for 1 h. The reaction was diluted withEtOAc and sat. NaHCO₃. The organic layer was washed with water andbrine, dried (Na₂SO₄), and concentrated. The crude was purified by flashcolumn chromatography on silica gel (EtOAc/hexanes, 0-70%) to give1-benzyl 5-(tert-butyl)6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylateas a yellow solid (28 mg, 56%). LC/MS (ESI) m/z: 619.4 (M+H)⁺.

Benzyl5-(((S)-2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate

To a solution of 1-benzyl 5-(tert-butyl)6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(28 mg, 0.045 mmol) in DCM (1 mL) was added TFA (1 mL). The reaction wasstirred at room temperature for 1 h and concentrated to give benzyl6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylateas a TFA salt, which was used directly without further purification.LC/MS (ESI) m/z=519.4 (M+H)⁺.

To a mixture of benzyl6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate(TFA salt, 0.045 mmol) in DCM (1 mL) was added DIEA (29 mg, 39 μL, 0.22mmol) at 0° C., followed by(S)-2-isocyanato-N,N-dimethyl-2-phenylethan-1-amine HCl salt (12 mg,0.054 mmol). The solution was stirred at 0° C. for 1 h and diluted withCHCl₃/i-PrOH (v/v 4:1) and washed with sat. NaHCO₃ and brine, dried(Na₂SO₄), and concentrated. The crude was purified by flash columnchromatography on silica gel (1.75 M NH₃ in MeOH/DCM, 0-10%) to givebenzyl5-(((S)-2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate (24 mg, 77% over 2 steps). LC/MS (ESI) m/z=709.4(M+H)⁺.

3-((1-(4-Aminobenzoyl)piperidin-3-yl)amino)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

A mixture of benzyl5-(((S)-2-(dimethylamino)-1-phenylethyl)carbamoyl)-6,6-dimethyl-3-((1-(4-nitrobenzoyl)piperidin-3-yl)amino)-5,6-dihydropyrrolo[3,4-c]pyrazole-1(4H)-carboxylate(24 mg, 0.034 mmol) and 10% Pd/C (5 mg) in MeOH (5 mL) was degassed. Themixture was stirred under H₂ (1 atm) at room temperature for 6 h. Thereaction was filtered through Celite® and concentrated to give3-((1-(4-aminobenzoyl)piperidin-3-yl)amino)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamideas a clear wax (18 mg, 70%). LC/MS (ESI) m/z: 545.4 (M+H)⁺.

Compound 115.3-((1-(4-acrylamidobenzoyl)piperidin-3-yl)amino)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

To a mixture of3-((1-(4-aminobenzoyl)piperidin-3-yl)amino)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide(18 mg, 0.033 mmol) in THF (1 mL) and sat. NaHCO₃ (1 mL) was addedacryloyl chloride (9.0 mg, 0.099 mmol) dropwise at 0° C. The mixture wasstirred at 0° C. for 10 min and diluted with CHCl₃/i-PrOH (v/v 4:1) andwashed with sat. NaHCO₃ and brine, dried (Na₂SO₄), and concentrated. Thecrude was dissolved in i-PrOH (1 mL) and LiOH (1 M, 1 mL) was added.After stirred at room temperature for 10 min, the mixture was dilutedwith CHCl₃/i-PrOH (v/v 4:1) and washed with sat. NaHCO₃ and brine, dried(Na₂SO₄), and concentrated. The crude was purified by reverse phasepreparative HPLC (MeOH/H₂O, 0-100%) to give3-((1-(4-acrylamidobenzoyl)piperidin-3-yl)amino)-N—((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamideTFA salt as a white solid (10.5 mg, 45%). ¹H NMR (TFA salt): 600 MHz(DMSO-d₆) δ 10.29 (s, 1H), 9.10 (s, 1H), 7.72-7.55 (m, 1H), 7.49-7.26(m, 7H), 6.73-6.61 (m, 1H), 6.49-6.40 (m, 1H), 6.27-6.24 (m, 1H),5.77-5.75 (m, 1H), 5.36-5.26 (m, 1H), 4.55-4.50 (m, 1H), 4.30-4.24 (m,2H), 3.55-3.45 (m, 3H), 3.38-3.32 (m, 2H), 3.28-3.07 (m, 2H), 2.88 (m,3H), 2.85 (m, 1H), 2.82 (m, 3H), 2.00-1.90 (m, 1H), 1.85-1.70 (m, 1H),1.65-1.50 (m, 6H), 1.09-1.03 (m, 1H); MS m/z: 599.4 [M+1].

TABLE 5 The following compounds were produced using the correspondingstarting compounds according to a method similar to that described forthe synthesis of Compound 115: Name Structure Characterization DataCompound 116 (S)-3-((1-(4- acrylamidobenzoyl) piperidin-4-yl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)- carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 11.30 (br, 1H), 10.30 (s, 1H), 7.71 (d, J =9.0 Hz, 2H), 7.36-7.33 (m, 4H), 7.28 (t, J = 7.8 Hz, 2H), 7.18 (t, J =7.8 Hz, 1H), 6.43 (dd, J = 16.8, 10.2 Hz, 1H), 6.27 (dd, J = 16.8, 2.2Hz, 1H), 5.95 (d, J = 6.0 Hz, 1H), 5.77 (dd, J = 10.2, 2.2 Hz, 1H),5.33-5.20 (m, 1H), 4.82 (q, J = 7.2 Hz, 1H), 4.26 (q, J = 12.0 Hz, 2H),3.72-3.58 (m, 1H), 3.16-3.03 (m, 2H), 2.60 (m, 1H), 2.42 (m, 1H), 2.19(s, 6H), 1.89 (m, 2H), 1.54 (s, 3H), 1.48 (s, 3H), 1.36 (m, 2H); MS m/z:599.4 [M + 1]. Compound 117 3-(((1R,3S)-3-(4- acrylamidobenzamido)cyclohexyl)amino)-N-((S)- 2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR (TFA salt): 600 MHz (DMSO-d₆) δ 10.35 (d, J = 3.0 Hz, 1H), 9.11(s, 1H), 8.09 (d, J = 7.8 Hz, 1H), 7.80 (dd, J = 9.0, 2.0 Hz, 2H), 7.71(dd, J = 9.0, 1.8 Hz, 2H), 7.46-7.42 (m, 2H), 7.39-7.35 (m, 2H), 7.30-7.28 (m, 1H), 6.68 (t, J = 7.8 Hz, 1H), 6.44 (dd, J = 16.8, 10.2 Hz,1H), 6.27 (dd, J = 16.8, 2.2 Hz, 1H), 5.78 (dd, J = 10.2, 2.2 Hz, 1H),5.34-5.30 (m, 1H), 4.52 (t, J = 12.0 Hz, 1H), 4.38 (dd, J = 13.2, 12.0Hz, 2H), 4.17-4.10 (m, 1H), 3.67 (m, 2H), 3.48 (t, J = 12.0 Hz, 2H),3.37-3.33 (m, 2H), 2.88 (m, 3H), 2.82 (m, 3H), 1.89-1.80 (m, 2H),1.71-1.60 (m, 3H), 1.62 (s, 3H), 1.55 (s, 3H), 1.36 (m, 2H); MS m/z:613.4 [M + 1]. Compound 118 3-(((1R,3R)-3-(4- acrylamidobenzamido)cyclohexyl)amino)-N- ((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 11.22 (br, 1H), 10.32 (s, 1H), 8.19 (dd, J= 7.8, 3.0 Hz, 1H), 7.81 (dd, J = 8.4, 3.0 Hz, 2H), 7.70 (dd, J = 8.4,5.4 Hz, 2H), 7.35 (d, J = 7.8 Hz, 2H), 7.30-7.26 (m, 2H), 7.20-7.16 (m,1H), 6.43 (dd, J = 16.8, 10.2 Hz, 1H), 6.27 (dd, J = 16.8, 2.2 Hz, 1H),6.01 (m, 1H), 5.77 (dd, J = 10.2, 2.2 Hz, 1H), 5.25-5.17 (m, 1H), 4.89-4.82 (m, 1H), 4.36-4.27 (m, 2H), 3.90-3.83 (m, 1H), 3.08- 3.01 (m, 1H),2.68-2.60 (m, 1H), 2.50-2.42 (m, 1H), 2.21 (s, 3H), 2.19 (s, 3H),2.13-2.08 (m, 1H), 1.92-1.86 (m, 1H), 1.85-1.79 (m, 1H), 1.78-1.73 (m,1H), 1.54 (s, 3H), 1.48 (d, J = 5.4 Hz, 3H), 1.42-1.35 (m, 1H),1.28-1.19 (m, 2H), 1.11- 1.03 (m, 1H); MS m/z: 613.4 [M + 1]. Compound119 (S)-3-((4-(4- acrylamidobenzamido) cyclohexyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 11.30 (br, 1H), 10.32 (s, 1H), 8.11 (d, J =7.8 Hz, 1H), 7.80 (d, J = 8.4 Hz, 2H), 7.71 (d, J = 8.4 Hz, 2H), 7.37(m, 2H), 7.32 (m, 2H), 7.22 (m, 1H), 6.43 (dd, J = 16.8, 10.2 Hz, 1H),6.27 (d, J = 16.8 Hz, 1H), 6.13 (m, 1H), 5.78 (d, J = 10.2, Hz, 1H),5.13-4.94 (m, 2H), 4.35-4.26 (m, 2H), 3.75- 3.49 (m, 1H), 3.47 (t, J =5.4 Hz, 1H), 3.40 (t, J = 5.4 Hz, 1H), 3.07-2.97 (m, 2H), 2.50- 2.32 (m,4H), 1.98 (d, J = 10.8 Hz, 3H), 1.87 (d, J = 10.2 Hz, 3H), 1.77-1.70 (m,1H), 1.67- 1.60 (m, 1H), 1.56 (s, 3H), 1.49 (s, 3H), 1.47-1.38 (m, 2H),1.37-1.33 (m, 1H), 1.29-1.17 (m, 4H), 1.15 (t, J = 7.2 Hz, 1H),0.85-0.76 (m, 1H); MS m/z: 613.4 [M + 1]. Compound 228. 3-(((1R,3S)-3-acrylamidocyclohexyl) amino)-N-((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 11.24 (br, 1H), 9.01 (br, 1H), 8.07 (m,1H), 7.40 (m, 2H), 7.35 (m, 2H), 7.26 (m, 1H), 6.52 (br, 1H), 6.17 (ddd,J = 17.0, 10.0, 1.2 Hz, 1H), 6.05 (ddd, J = 17.0, 7.0, 1.8 Hz, 1H), 5.55(ddd, J = 10.0, 7.6, 2.4 Hz, 1H), 5.20 (m, 1H), 4.42 (m, 1H), 4.31 (m,1H), 3.69 (m, 1H), 2.98 (m, 1H), 2.76 (m, 6H), 2.03 (m, 1H), 1.87 (m,1H), 1.76 (m, 2H), 1.56 (s, 3H), 1.48 (s, 3H), 1.32 (m, 1H), 1.08 (m,2H); MS m/z: 494.4 [M + 1]. Compound 229. 3-(((1R,3R)-3-acrylamidocyclohexyl)amino)- N-((S)-2-(dimethylamino)-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 11.13 (br, 1H), 9.00 (br, 1H), 7.96 (m,1H), 7.40 (t, J = 7.6 Hz, 2H), 7.36 (t, J = 7.0 Hz, 2H), 7.27 (t, J =7.0 Hz, 1H), 6.52 (br, 1H), 6.25 (ddd, J = 17.0, 10.6, 7.0 Hz, 1H), 6.04(ddd, J = 17.0, 3.5, 2.4 Hz, 1H), 5.53 (ddd, J = 10.0, 10.0, 2.4 Hz,1H), 5.27 (m, 1H), 4.43 (m, 1H), 4.30 (t, J = 11.2 Hz, 1H), 4.01 (m,1H), 3.50 (m, 1H), 2.78 (m, 6H), 1.74 (m, 2H), 1.61 (m, 1H), 1.57 (s,3H), 1.52 (m, 3H), 1.48 (s, 3H), 1.22 (m, 2H); MS m/z: 494.4 [M + 1].Compound 230. (S)-3-((4- acrylamidocyclohexyl)amino)-N-(2-(dimethylamino)-1- phenylethyl)-6,6-dimethyl-4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)- carboxamide

¹H NMR (mixture of diastereomers): 600 MHz (DMSO-d₆) δ 11.28 (br, 1H),9.04 (s, 1H), 7.94 (dd, J = 18.8, 7.6 Hz, 1H), 7.41 (d, J = 7.6 Hz, 2H),7.36 (t, J = 7.0 Hz, 2H), 7.27 (t, J = 7.6 Hz, 1H), 6.58 (br, 1H), 6.28(dd, J = 17.0, 10.6 Hz, 1H for one isomer), 6.20 (dd, J = 17.0, 10.0 Hz,1H for another isomer), 6.05 (ddd, J = 17.0, 4.7, 2.4 Hz, 1H), 5.54 (dd,J = 10.0, 2.4 Hz, 1H), 5.29 (br, 1H), 4.42 (dd, J = 23.5, 10.0 Hz, 1H),4.29 (dd, J = 27.0, 11.2 Hz, 1H), 3.72 (m, 1H), 3.55 (m, 1H), 3.20 (m,1H), 2.97 (m, 1H), 2.81 (m, 6H), 1.94 (m, 1H), 1.83 (m, 1H), 1.61 (m,2H), 1.57 (s, 3H), 1.49 (s, 3H for one isomer), 1.48 (s, 3H for anotherisomer), 1.23 (m, 2H); MS m/z: 494.4 [M + 1]. Compound 231.(5)-3-((1-acryloylpiperidin- 4-yl)amino)-N-(2- (dimethylamino)-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 11.30 (br, 1H), 7.34 (d, J = 7.6 Hz, 2H),7.29 (t, J = 7.0 Hz, 2H), 7.19 (t, J = 7.0 Hz, 1H), 6.81 (dd, J = 17.0,10.6 Hz, 1H), 6.08 (dd, J = 17.0, 2.9 Hz, 1H), 5.98 (br, 1H), 5.65 (dd,J = 10.0, 2.4 Hz, 1H), 4.86 (m, 1H), 4.27 (m, 2H), 4.20 (d, J = 13.0 Hz,1H), 3.95 (d, J = 13.5 Hz, 1H), 3.19 (t, J = 12.3 Hz, 1H), 2.91 (t, J =11.2 Hz, 1H), 2.22 (m, 6H), 1.88 (m, 2H), 1.55 (s, 3H), 1.48 (s, 3H),1.28 (m, 2H); MS m/z: 480.3 [M + 1]. Compound 232.3-((1-acryloylpiperidin-3- yl)amino)-N-((S)-2- (dimethylamino)-1-phenylethyl)-6,6-dimethyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 11.29 (br, 1H), 7.33 (m, 2H), 7.28 (m, 2H),7.19 (m, 1H), 6.81 (m, 1H), 6.63 (dd, J = 16.4, 10.6 Hz, 1H), 6.10 (dd,J = 15.9, 5.9 Hz, 1H), 6.02 (d, J = 17.0 Hz, 1H), 5.96 (m, 1H), 5.66 (d,J = 9.4 Hz, 1H), 5.56 (dd, J = 18.8, 12.3 Hz, 1H), 5.31 (m, 1H), 4.84(m, 1H), 4.36 (m, 1H), 4.25 (m, 2H), 4.01 (m, 1H), 3.86 (m, 2H), 3.19(m, 1H), 3.06 (m, 1H), 2.64 (m, 2H), 2.20 (m, 6H), 1.95 (m, 1H), 1.73(m, 1H), 1.55 (s, 3H), 1.48 (d, J = 5.9 Hz, 3H), 1.43 (m, 2H); MS m/z:480.3 [M + 1].

Example 5.(S)-3′-(4-acrylamidobenzamido)-N-(2-(dimethylamino)-1-phenylethyl)-1′,4′-dihydro-5′H-spiro[cyclopropane-1,6′-pyrrolo[3,4-c]pyrazole]-5′-carboxamide(Compound 233)

The synthesis of Compound 233 follows Synthetic Scheme 5. The synthesesof Compounds 234-240 (presented in Table 6) follow a correspondingmethod.

TABLE 6 The following compounds were produced using the correspondingstarting compounds according to a method similar to that described forthe synthesis of Compound 233. Name Structure Characterization DataCompound 233. (S)-3′-(4- acrylamidobenzamido)-N- (2-(dimethylamino)-1-phenylethyl)-1′,4′-dihydro- 5′H-spiro[cyclopropane-1,6′-pyrrolo[3,4-c]pyrazole]- 5′-carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 12.16 (br, 1H), 10.79 (s, 1H), 10.44 (s,1H), 8.00 (m, 2H), 7.79 (m, 2H), 7.36 (m, 2H), 7.30 (m, 2H), 7.21 (m,1H), 6.46 (dd, J = 17.0, 10.0 Hz, 1H), 6.29 (dd, J = 17.0, 1.8 Hz, 1H),5.80 (dd, J = 10.0, 1.8 Hz, 1H), 4.89 (m, 1H), 4.70 (m, 2H), 2.27 (m,6H), 2.05 (m, 1H), 1.99 (m, 1H), 0.82 (m, 4H); MS m/z: 514.3 [M + 1].Compound 234. (R)-3-(4- acrylamidobenzamido)-N-((S)-2-(dimethylamino)-1- phenylethyl)-6-isopropyl-4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)- carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 12.42 (br, 1H), 10.77 (s, 1H), 10.45 (s,1H), 8.00 (d, J = 8.2 Hz, 2H), 7.79 (d, J = 8.2 Hz, 2H), 7.38 (m, 2H),7.32 (m, 2H), 7.22 (m, 1H), 6.60 (br, 1H), 6.47 (dd, J = 17.0, 10.0 Hz,1H), 6.29 (dd, J = 17.0, 2.4 Hz, 1H), 5.79 (dd, J = 10.6, 1.8 Hz, 1H),1.83 (m, 1H), 4.54 (m, 2H), 2.33 (m, 6H), 0.98 (d, J = 5.3 Hz, 3H), 0.84(m, 1H), 0.49 (d, J = 6.5 Hz, 3H); MS m/z: 530.3 [M + 1]. Compound 235.(S)-3-(4- acrylamidobenzamido)-N- ((S)-2-(dimethylamino)-1-phenylethyl)-6-isopropyl- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 600 MHz (DMSO- d₆) δ 12.40 (br, 1H), 10.76 (s, 1H), 10.44 (s,1H), 8.00 (d, J = 7.6 Hz, 2H), 7.78 (d, J = 7.6 Hz, 2H), 7.35 (m, 2H),7.30 (m, 2H), 7.20 (m, 1H), 6.56 (br, 1H), 6.47 (dd, J = 17.0, 10.0 Hz,1H), 6.29 (dd, J = 17.0, 1.8 Hz, 1H), 5.80 (dd, J = 10.0, 1.8 Hz, 1H),4.97 (m, 1H), 4.79 (m, 1H), 4.53 (m, 2H), 2.37 (m, 6H), 1.00 (m, 3H),0.84 (m, 1H), 0.55 (d, J = 7.0 Hz, 3H); MS m/z: 530.3 [M + 1]. Compound236. (S)-3′-(4-acrylamidobenzamido)- N-(2-(dimethylamino)-1-phenylethyl)-1′,4′-dihydro-5′H- spiro(cyclohexane-1,6′-pyrrolo[3,4-c]pyrazole]-5′- carboxamide

¹H NMR: 500 MHz (DMSO-d₆) δ 12.40 (br, 1H), 10.83 (s, 1H), 10.48 (s,1H), 8.06 (d, J = 8.5 Hz, 2H), 7.86 (d, J = 8.5 Hz, 2H), 7.42 (d, J =7.3 Hz, 2H), 7.35 (t, J = 7.3 Hz, 2H), 7.25 (t, J = 7.3 Hz, 1H), 6.53(dd, J = 17.0, 10.0 Hz, 1H), 6.37 (dd, J = 17.0, 1.8 Hz, 1H),6.27 (m,1H), 5.88 (dd, J = 10.0, 1.8 Hz, 1H), 4.92 (m, 1H), 4.59 (m, 2H), 2.87(m, 1H), 2.74 (m, 2H), 2.46 (m, 1H), 2.25 (s, 6H), 1.69 (m, 4H), 1.53(m, 2H), 1.42 (m, 2H), 1.29 (s, 6H), 1.21 (m, 2H), 0.91 (m, 2H); MS m/z:556.3 [M + 1]. Compound 237. (R)-3-(4-acrylamidobenzamido)-N-((S)-2-(dimethylamino)-1- phenylethyl)-6-phenyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR (a mixture of two rotamers): 500 MHz (DMSO-d₆) δ 12.33, 12.14 (s,1H), 10.84, 10.73 (s, 1H), 10.35 (s, 1H), 7.95 (m, 2H), 7.73 (m, 2H),7.23 (m, 9H), 7.10 (t, J = 7.3 Hz, 1H), 6.40 (dd, J = 17.1, 10.1 Hz,1H), 6.24 (dd, J = 16.8, 1.8 Hz, 1H), 5.93 (m, 1H), 5.74 (dd, J = 10.1,1.8 Hz, 1H), 4.73 (m, 1H), 4.61 (m, 2H), 2.21 (m, 1H), 1.99 (m, 6H); MSm/z: 564.3 [M + 1]. Compound 238. (R)-3-(4-acrylamidobenzamido)-N-((S)-2-(dimethylamino)-1- phenylethyl)-6-phenyl-4,6-dihydropyrrolo[3,4-c]pyrazole- 5(1H)-carboxamide

¹H NMR: 500 MHz (DMSO-d₆) δ 12.33 (s, 1H), 10.75 (s, 1H), 10.35 (s, 1H),7.95 (m, 2H), 7.73 (m, 2H), 7.21 (m, 10H), 6.40 (dd, J = 17.1, 10.0 Hz,1H), 6.24 (dd, J = 17.1, 1.8 Hz, 1H), 5.87 (m, 1H), 5.75 (dd, J = 10.1,1.8 Hz, 1H), 4.72 (m, 2H), 4.61 (m, 1H), 2.57 (m, 1H), 2.31 (m, 1H),2.11 (s, 6H); MS m/z: 564.3 [M + 1]. Compound 239.(S)-3-(4-acrylamidobenzamido)- N-((S)-2-(dimethylamino)-1-phenylethyl)-6-phenyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

¹H NMR (a mixture of two rotamers): 500 MHz (DMSO-d₆) δ 12.34, 12.10 (s,1H), 10.74 (s, 1H), 10.35 (s, 1H), 7.95 (m, 2H), 7.73 (m, 2H), 7.20 (m,10H), 6.40 (dd, J = 17.1, 10.1 Hz, 1H), 6.24 (dd, J = 17.1, 1.8 Hz, 1H),5.93 (m, 1H), 5.74 (dd, J = 10.1, 1.8 Hz, 1H), 4.73 (m, 1H), 4.61 (m,2H), 2.23 (m, 1H), 2.00 (m, 6H); MS m/z: 564.3 [M + 1]. Compound 240.(S)-3-(4-acrylamidobenzamido)- N-((S)-2-(dimethylamino)-1-phenylethyl)-6-phenyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

¹H NMR: 500 MHz (DMSO-d₆) δ 12.37 (s, 1H), 10.77 (s, 1H), 10.42 (s, 1H),7.96 (m, 2H), 7.75 (m, 2H), 7.20 (m, 10H), 6.43 (dd, J = 17.1, 10.1 Hz,1H), 6.24 (dd, J = 17.1, 1.8 Hz, 1H), 5.90 (m, 1H), 5.75 (dd, J = 10.1,1.8 Hz, 1H), 4.42 (m, 6H), 1.19 (m, 1H); MS m/z: 564.3 [M + 1].

The synthesis of Compound 241 follows Synthetic Scheme 6. The synthesesof Compounds 242-247 (presented in Table 7) follow a correspondingmethod.

t-Butyl6,6-dimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylate

To a solution of 5-(tert-butyl) ethyl6,6-dimethyl-3-((3-nitrophenyl)amino)-4,6-dihydropyrrolo[3,4-c]pyrazole-1,5-dicarboxylate(500 mg, 1.05 mmol) in i-PrOH (5 mL) was added 1 M NaOH aqueous solution(5 mL). The mixture was stirred at rt for 30 min and extracted withCHCl₃/i-PrOH (v:v 4:1). The crude was purified by flash columnchromatography on silica gel (1.75 M NH₃ in MeOH/DCM, 0-15%) to givet-butyl6,6-dimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylateas a yellow solid (394 mg, 93%). LC/MS (ESI) m/z: 402.4 (M+H)⁺.

t-Butyl1,6,6-trimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylate

A solution of t-butyl6,6-dimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylate(394 mg, 0.98 mmol) and methyl iodide (697 mg, 0.31 mL, 4.91 mmol) inTHF (5 mL) was stirred at 80° C. overnight. The mixture was cooled andextracted with EtOAc and washed with sat. NaHCO₃ and brine. The crudewas purified by reverse phase preparative HPLC (MeOH/H₂O, 0-100%) togive t-butyl1,6,6-trimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylate(123 mg, 30%) and t-butyl2,6,6-trimethyl-3-(3-nitrobenzamido)-2,6-dihydropyrrolo[3,4-c]pyrazole-5(4H)-carboxylate(108 mg, 26%) as white solids. LC/MS (ESI) m/z: 416.4 (M+H)⁺.

Example 41.(S)-3-(3-acrylamidobenzamido)-N-(2-(dimethylamino)-1-phenylethyl)-1,6,6-trimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamide

Following the previous described procedure starting with t-butyl1,6,6-trimethyl-3-(3-nitrobenzamido)-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxylate,(S)-3-(3-acrylamidobenzamido)-N-(2-(dimethylamino)-1-phenylethyl)-1,6,6-trimethyl-4,6-dihydropyrrolo[3,4-c]pyrazole-5(1H)-carboxamidewas obtained as a white solid. ¹H NMR: 500 MHz (DMSO-d₆) δ 10.70 (s,1H), 10.34 (s, 1H), 7.94 (d, J=8.9 Hz, 2H), 7.71 (d, J=8.9 Hz, 2H), 7.31(d, J=7.3 Hz, 2H), 7.23 (t, J=7.6 Hz, 2H), 7.13 (t, J=7.3 Hz, 1H), 6.40(dd, J=17.1, 10.1 Hz, 1H), 6.24 (dd, J=17.1, 1.8 Hz, 1H), 6.21 (m, 1H),5.74 (dd, J=10.1, 1.8 Hz, 1H), 4.81 (q, J=7.3 Hz, 1H), 4.45 (dd, J=15.9,11.9 Hz, 1H), 3.65 (s, 3H), 2.60 (m, 1H), 2.33 (m, 1H), 2.13 (s, 6H),1.64 (s, 3H), 1.56 (s, 3H); MS m/z: 530.3 [M+1].

TABLE 7 The following compounds were produced using the correspondingstarting compounds according to a method similar to that described forthe synthesis of Compound 241: Name Structure Characterization DataCompound 242 (S)-3-(4- acrylamidobenzamido)-N- (2-(dimethylamino)-1-phenylethyl)-2,6,6- trimethyl-2,6- dihydropyrrolo[3,4- c]pyrazole-5(4H)-carboxamide

¹H NMR: 500 MHz (DMSO- d₆) δ 10.40 (s, 1H), 10.22 (s, 1H), 7.93 (d, J =8.9 Hz, 2H), 7.77 (d, J = 8.9 Hz, 2H), 7.28 (d, J = 7.3 Hz, 2H), 7.22(t, J = 7.6 Hz, 2H), 7.12 (t, J = 7.3 Hz, 1H), 6.41 (dd, J = 17.1, 10.1Hz, 1H), 6.24 (dd, J = 17.1, 1.8 Hz, 1H), 6.14 (d, J = 7.3 Hz, 1H), 5.75(dd, J = 10.1, 1.8 Hz, 1H), 4.81 (q, J = 7.9 Hz, 1H), 4.34 (dd, J =15.3, 12.5 Hz, 1H), 3.67 (s, 3H), 2.57 (m, 1H), 2.30 (m, 1H), 2.12 (s,6H), 1.53 (s, 3H), 1.46 (s, 3H); MS m/z: 530.3 [M + 1]. Compound 243.(S)-3-(4-acrylamido-2- methoxybenzamido)-N-(2- (dimethylamino)-1-phenylethyl)-1,6,6- trimethyl-4,6- dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 500 MHz (DMSO- d₆) δ 10.40 (s, 1H), 10.01 (s, 1H), 7.79 (d, J =8.5 Hz, 1H), 7.58 (dd, J = 1.5 Hz, 1H), 7.32 (m, 2H), 7.25 (t, J = 7.3Hz, 2H), 7.16 (t, J = 7.3 Hz, 1H), 6.40 (dd, J = 17.1, 10.1 Hz, 1H),6.37 (br, 1H), 6.25 (dd, J = 16.8, 1.8 Hz, 1H), 5.76 (dd, J = 10.1, 1.8Hz, 1H), 4.92 (m, 1H), 4.49 (m, 2H), 3.89 (s, 3H), 3.64 (s, 3H), 2.30(m, 6H), 1.64 (s, 3H), 1.57 (s, 3H); MS m/z: 560.3 [M + 1]. Compound244. (S)-3-(4-acrylamido-2- methoxybenzamido)-N-(2- (dimethylamino)-1-phenylethyl)-2,6,6- trimethyl-2,6- dihydropyrrolo[3,4- c]pyrazole-5(4H)-carboxamide

¹H NMR: 500 MHz (DMSO- d₆) δ 10.52 (s, 1H), 10.01 (s, 1H), 7.79 (d, J =8.5 Hz, 1H), 7.65 (dd, J = 1.8 Hz, 1H), 7.31 (d, J = 8.5 Hz, 2H), 7.24(t, J = 7.6 Hz, 2H), 7.14 (t, J = 7.3 Hz, 1H), 6.43 (dd, J = 16.8, 10.1Hz, 1H), 6.25 (br, 1H), 6.25 (dd, J = 16.8, 1.8 Hz, 1H), 5.76 (dd, J =10.1, 1.8 Hz, 1H), 4.89 (m, 1H), 4.41 (m, 2H), 3.90 (s, 3H), 3.67 (s,3H), 2.23 (m, 6H), 1.54 (s, 3H), 1.46 (s, 3H); MS m/z: 560.3 [M + 1].Compound 245. 3-(4-acrylamidobenzamido)- N-(1- (dimethylamino)propan-2-yl)-1,6,6-trimethyl-4,6- dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 500 MHz (DMSO- d₆) δ 10.68 (s, 1H), 10.33 (s, 1H), 7.93 (d, J =8.9 Hz, 2H), 7.71 (d, J = 8.9 Hz, 2H), 6.39 (dd, J = 17.1, 10.1 Hz, 1H),6.23 (dd, J = 17.1, 1.8 Hz, 1H), 5.74 (dd, J = 10.1, 1.8 Hz, 1H), 5.64(d, J = 7.9 Hz, 1H), 4.33 (dd, J = 21.7, 11.9 Hz, 2H), 3.74 (m, 1H),3.66 (s, 3H), 2.20 (dd, J = 11.9, 7.0 Hz, 1H), 2.10 (m, 1H), 2.08 (s,6H), 1.64 (s, 6H), 1.00 (d, J = 6.4 Hz, 3H); MS m/z: 530.3 [M + 1].Compound 246. (S)-2-(dimethylamino)-1- phenylethyl 3-(4-acrylamidobenzamido)- 1,6,6-trimethyl-4,6- dihydropyrrolo[3,4-c]pyrazole-5(1H)- carboxylate

¹H NMR (a mixture of two rotamers): 500 MHz (DMSO- d₆) δ 10.74, 10.70(s, 1H), 10.33, 10.32 (s, 1H),7.93 (m, 2H), 7.69 (m, 2H), 7.32 (m, 4H),7.23 (m, 1H), 6.39 (m, 1H), 6.23 (m, 1H), 5.75 (m, 1H), 4.56 (dd, J =15.3, 13.4 Hz, 2H), 4.40, 4.31 (d, J = 13.4 Hz, 1H), 3.68, 3.67 (s, 3H),2.73 (m, 1H), 2.45 (m, 1H), 2.17, 2.15 (s, 6H), 1.73, 1.55 (s, 3H), 1.64(s, 3H); MS m/z: 531.3 [M + 1]. Compound 247.(S)-N-(2-(dimethylamino)-1- phenylethyl)-1,6,6- trimethyl-3-(4-propionamidobenzamido)- 4,6-dihydropyrrolo[3,4- c]pyrazole-5(1H)-carboxamide

¹H NMR: 500 MHz (DMSO- d₆) δ 10.79 (s, 1H), 10.18 (s, 1H), 8.03 (d, J =8.9 Hz, 2H), 7.76 (d, J = 8.9 Hz, 2H), 7.43 (d, J = 7.3 Hz, 2H), 7.35(t, J = 7.3 Hz, 2H), 7.25 (t, J = 7.3 Hz, 1H), 6.34 (d, J = 7.3 Hz, 1H),4.93 (q, J = 7.9 Hz, 1H), 4.56 (dd, J = 16.5, 11.9 Hz, 2H), 3.78 (s,3H), 2.72 (m, 1H), 2.45 (m, 1H), 2.42 (q, J = 7.6 Hz, 2H), 2.25 (s, 6H),1.77 (s, 3H), 1.69 (s, 3H), 1.16 (t, J = 7.3 Hz, 3H); MS m/z: 532.4 [M +1].

Biological Assays of the Compounds Example 5. Inhibition of KinaseActivity

Compounds of the invention were assayed for activity against a varietyof different kinases. Exemplary results are presented as calculated IC₅₀values (Table A1 & A2). In Table A1 and A2 “A” represents a calculatedIC₅₀ value of less than 100 nM; “B” represents a calculated IC₅₀ valueof greater than or equal to 100 nM and less than 1 μM; and “C”represents a calculated IC₅₀ value of 1 μM or greater. The co-factorsused for each kinase in the assays were as follows: CDK7: cyclin H andMNAT1; CDK2: cyclin A; CDK9: cyclin K.

TABLE A1 Calculated IC₅₀ values of exemplary compounds of the inventionagainst CDK7. Compound No. CDK7 IC₅₀ 101 A 102 A 103 A 104 A 105 A 106 B107 A 108 A 109 A 110 A 111 B 112 A 113 A 114 A 115 A 116 A 117 A 118 A119 A 120 A 123 A 214 A 215 A 216 A 217 A 222 A 231 A 232 A 233 A 234 A235 C 236 B 237 C 238 C 239 C 240 C 241 A 242 C 243 C 244 C 245 C 246 B

TABLE A2 Calculated IC₅₀ values of exemplary compounds of the inventionagainst various kinases. Compound No. Kinase 101 106 CDK2 C CDK9 C CHEK2A FGR A HIPK4 B PRKCQ A RET A SRC A MELK B B

Example 6. Inhibition of Cell Proliferation

Exemplary compounds of the invention were tested at differentconcentrations. Cells were plated in 96-well plates at the followingseeding densities: Jurkat T-cell acute lymphoblastic leukemia 25,000cells/well; HCT116 colorectal carcinoma 8,000 cells/well; Kellyneuroblastoma 4,000 cells/well. The cells were treated with variousconcentration of compounds (ranging from 1 nM to 10 μM). DMSO solventwith no compound served as a control. Following incubation for 72 hours,cell survival following treatment with exemplary compounds describedherein was assessed by CellTiter-Glo® Luminescent cell viability assay(Promega). IC₅₀ values were determined using GRAPHPAD PRISM 6 software.Exemplary results are shown in Table A3, wherein “A” represents acalculated IC₅₀ value of less than 500 nM; “B” represents a calculatedIC₅₀ value of greater than or equal to 500 nM and less than 5000 μM; and“C” represents a calculated IC₅₀ value of 5000 μM or greater

TABLE A3 Calculated IC₅₀ values of exemplary compounds of the inventionagainst cancer cells. Jurkat T-cell HCT116 Compound acute lymphoblasticcolorectal Kelly No. leukemia carcinoma neuroblastoma 101 A A B 102 C104 B B 106 C 107 B 112 B

Example 7. Labeling of CDK7 with an Inhibitor

CAK complex (Millipore cat#14-476) in 40 mM Hepes pH 7.4, 150 mM NaCl,5% glycerol and 1 mM DTT with protease and phosphatase inhibitors wasincubated with a 10-fold molar excess of Compound 101 for 6 hrs at 37°C. Proteins were resolved by SDS-PAGE, bands corresponding to CDK7 weredigested in-gel with trypsin, and peptides analyzed by nano LC-MS usingan Orbitrap XL mass spectrometer (ThermoFisher Scientific, San Jose,Calif.). Efficiency of labeling was estimated from the reduction insignal of the Cys312 containing peptide YFSNRPGPTPGCQLPRPNCPVETLKcompared to DMSO control. Signals from CDK7 peptides VPFLPGDSDLDQLTR andLDFLGEGQFATVYK were used for normalization. See FIG. 1 for the total ionchromatograms (TIC) and extracted ion chromatograms (EIC) of the CDK7peptides treated with DMSO (A-D) or Compound 101 (E-H). The labeledpeptide was detected by mass spectrometry, as shown in the spectrum ofFIG. 2. The signal at m/z 687.7498 corresponds toYFSNRPGPTPGCQLPRPNCPVETLK, labeled with Compound 101 at Cys312.

EQUIVALENTS AND SCOPE

In the claims articles such as “a,” “an,” and “the” may mean one or morethan one unless indicated to the contrary or otherwise evident from thecontext. Claims or descriptions that include “or” between one or moremembers of a group are considered satisfied if one, more than one, orall of the group members are present in, employed in, or otherwiserelevant to a given product or process unless indicated to the contraryor otherwise evident from the context. The invention includesembodiments in which exactly one member of the group is present in,employed in, or otherwise relevant to a given product or process. Theinvention includes embodiments in which more than one, or all of thegroup members are present in, employed in, or otherwise relevant to agiven product or process.

Furthermore, the invention encompasses all variations, combinations, andpermutations in which one or more limitations, elements, clauses, anddescriptive terms from one or more of the listed claims is introducedinto another claim. For example, any claim that is dependent on anotherclaim can be modified to include one or more limitations found in anyother claim that is dependent on the same base claim. Where elements arepresented as lists, e.g., in Markush group format, each subgroup of theelements is also disclosed, and any element(s) can be removed from thegroup. It should it be understood that, in general, where the invention,or aspects of the invention, is/are referred to as comprising particularelements and/or features, certain embodiments of the invention oraspects of the invention consist, or consist essentially of, suchelements and/or features. For purposes of simplicity, those embodimentshave not been specifically set forth in haec verba herein. It is alsonoted that the terms “comprising” and “containing” are intended to beopen and permits the inclusion of additional elements or steps. Whereranges are given, endpoints are included. Furthermore, unless otherwiseindicated or otherwise evident from the context and understanding of oneof ordinary skill in the art, values that are expressed as ranges canassume any specific value or sub-range within the stated ranges indifferent embodiments of the invention, to the tenth of the unit of thelower limit of the range, unless the context clearly dictates otherwise.

This application refers to various issued patents, published patentapplications, journal articles, and other publications, all of which areincorporated herein by reference. If there is a conflict between any ofthe incorporated references and the instant specification, thespecification shall control. In addition, any particular embodiment ofthe present invention that falls within the prior art may be explicitlyexcluded from any one or more of the claims. Because such embodimentsare deemed to be known to one of ordinary skill in the art, they may beexcluded even if the exclusion is not set forth explicitly herein. Anyparticular embodiment of the invention can be excluded from any claim,for any reason, whether or not related to the existence of prior art.

Those skilled in the art will recognize or be able to ascertain using nomore than routine experimentation many equivalents to the specificembodiments described herein. The scope of the present embodimentsdescribed herein is not intended to be limited to the above Description,but rather is as set forth in the appended claims. Those of ordinaryskill in the art will appreciate that various changes and modificationsto this description may be made without departing from the spirit orscope of the present invention, as defined in the following claims.

1. A compound of Formula (I):

or a pharmaceutically acceptable salt thereof, wherein: R¹ is—NR^(a)R^(b), —CHR^(a)R^(b) or —OR^(a), wherein each of R^(a) and R^(b)is independently hydrogen, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, or an oxygenprotecting group when attached to an oxygen atom, or R^(a) and R^(b) arejoined to form an optionally substituted carbocyclic, optionallysubstituted heterocyclic, optionally substituted aryl, or optionallysubstituted heteroaryl ring; each of R³ and R⁴ is independentlyhydrogen, halogen, optionally substituted C₁-C₆ alkyl, or optionallysubstituted aryl, or R³ and R⁴ are joined to form an optionallysubstituted C₃-C₆ carbocyclyl ring; R⁵ is independently hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protecting group; L¹is —NR^(L1)—, —NR^(L1)C(═O)—, —C(═O)NR^(L1)-, —O—, or —S—, whereinR^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group; Ring A is optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl; L² is a bond, —C(═O)—, —NR^(L2)—,—C(═O)NR^(L2)—, —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protection group; RingB is absent, optionally substituted carbocyclyl, optionally substitutedheterocyclyl, optionally substituted aryl, or optionally substitutedheteroaryl; and R² is any of Formulae (i-1)-(i-42):

wherein: L³ is a bond or an optionally substituted C₁₋₄ hydrocarbonchain, optionally wherein one or more carbon units of the hydrocarbonchain are independently replaced with —C═O—, —O—, —S—, —NR^(L3a)—,—NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—, —OC(═O)—,—C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—,cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—,—S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—, —S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—,—S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—, wherein R^(L3a) is hydrogen,substituted or unsubstituted C₁₋₆ alkyl, or a nitrogen protecting group,and wherein each occurrence of R^(L3b) is independently hydrogen,halogen, optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl, or two R^(L3b) groups are joined toform an optionally substituted carbocyclic or optionally substitutedheterocyclic ring; L⁴ is a bond or an optionally substituted, branchedor unbranched C₁₋₆ hydrocarbon chain; each of R^(E1), R^(E2), and R^(E3)is independently hydrogen, halogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl, —CN,—CH₂OR^(EE), —CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂,—Si(R^(EE))₃, and —SR^(EE), wherein each occurrence of R^(EE) isindependently hydrogen, optionally substituted alkyl, optionallysubstituted alkoxy, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl, or two R^(EE) groups are joined to form anoptionally substituted heterocyclic ring; or R^(E1) and R^(E3), orR^(E2) and R^(E3), or R^(E1) and R^(E2) are joined to form an optionallysubstituted carbocyclic or optionally substituted heterocyclic ring;R^(E4) is a leaving group; R^(E5) is halogen; R^(E6) is hydrogen,substituted or unsubstituted C₁₋₆ alkyl, or a nitrogen protecting group;each instance of Y is independently O, S, or NR^(E7), wherein R^(E7) ishydrogen, substituted or unsubstituted C₁₋₆ alkyl, or a nitrogenprotecting group; a is 1 or 2; and each instance of z is independently0, 1, 2, 3, 4, 5, or 6, as valency permits.
 2. The compound of claim 1,wherein the compound is of Formula (I):

or a pharmaceutically acceptable salt thereof, wherein: R¹ is—NR^(a)R^(b), —CHR^(a)R^(b) or —OR^(a), wherein each of R^(a) and R^(b)is independently hydrogen, optionally substituted alkyl, optionallysubstituted alkenyl, optionally substituted alkynyl, optionallysubstituted carbocyclyl, optionally substituted heterocyclyl, optionallysubstituted aryl, optionally substituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, or an oxygenprotecting group when attached to an oxygen atom, or R^(a) and R^(b) arejoined to form an optionally substituted carbocyclic, optionallysubstituted heterocyclic, optionally substituted aryl, or optionallysubstituted heteroaryl ring; each of R³ and R⁴ is independentlyhydrogen, halogen, or optionally substituted C₁-C₆ alkyl, or R³ and R⁴are joined to form an optionally substituted C₃-C₆ carbocyclyl ring; R⁵is hydrogen, optionally substituted C₁-C₆ alkyl, or a nitrogenprotecting group; L¹ is —NR^(L1)-, —NR^(L1)C(═O)—, —C(═O)NR^(L1)-, —O—,or —S—, wherein R^(L1) is hydrogen, optionally substituted C₁-C₆ alkyl,or a nitrogen protecting group; Ring A is optionally substitutedcarbocyclyl, optionally substituted heterocyclyl, optionally substitutedaryl, or optionally substituted heteroaryl; L² is a bond, —C(═O)—,—C(═O)NR^(L2)—, —NR^(L2)C(═O)—, —O—, or —S—, wherein R^(L2) is hydrogen,optionally substituted C₁-C₆ alkyl, or a nitrogen protection group; RingB is absent, optionally substituted carbocyclyl, optionally substitutedheterocyclyl, optionally substituted aryl, or optionally substitutedheteroaryl; and R² is any of Formulae (i-1)-(i-41):

wherein: L³ is a bond or an optionally substituted C₁₋₄ hydrocarbonchain, optionally wherein one or more carbon units of the hydrocarbonchain are independently replaced with —C═O—, —O—, —S—, —NR^(L3a)—,—NR^(L3a)C(═O)—, —C(═O)NR^(L3a)—, —SC(═O)—, —C(═O)S—, —OC(═O)—,—C(═O)O—, —NR^(L3a)C(═S)—, —C(═S)NR^(L3a)—, trans-CR^(L3b)═CR^(L3b)—,cis-CR^(L3b)═CR^(L3b)—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—,—S(═O)NR^(L3a)—, —NR^(L3a)S(═O)—, —S(═O)₂—, —S(═O)₂O—, —OS(═O)₂—,—S(═O)₂NR^(L3a)—, or —NR^(L3a)S(═O)₂—, wherein R^(L3a) is hydrogen,substituted or unsubstituted C₁₋₆ alkyl, or a nitrogen protecting group,and wherein each occurrence of R^(L3b) is independently hydrogen,halogen, optionally substituted alkyl, optionally substituted alkenyl,optionally substituted alkynyl, optionally substituted carbocyclyl,optionally substituted heterocyclyl, optionally substituted aryl, oroptionally substituted heteroaryl, or two R^(L3b) groups are joined toform an optionally substituted carbocyclic or optionally substitutedheterocyclic ring; L⁴ is a bond or an optionally substituted, branchedor unbranched C₁₋₆ hydrocarbon chain; each of R^(E1), R^(E2), and R^(E3)is independently hydrogen, halogen, optionally substituted alkyl,optionally substituted alkenyl, optionally substituted alkynyl,optionally substituted carbocyclyl, optionally substituted heterocyclyl,optionally substituted aryl, optionally substituted heteroaryl, —CN,—CH₂OR^(EE), —CH₂N(R^(EE))₂, —CH₂SR^(EE), —OR^(EE), —N(R^(EE))₂,—Si(R^(EE))₃, and —SR^(EE), wherein each occurrence of R^(EE) isindependently hydrogen, optionally substituted alkyl, optionallysubstituted alkoxy, optionally substituted alkenyl, optionallysubstituted alkynyl, optionally substituted carbocyclyl, optionallysubstituted heterocyclyl, optionally substituted aryl, or optionallysubstituted heteroaryl, or two R^(EE) groups are joined to form anoptionally substituted heterocyclic ring; or R^(E1) and R^(E3), orR^(E2) and R^(E3), or R^(E1) and R^(E2) are joined to form an optionallysubstituted carbocyclic or optionally substituted heterocyclic ring;R^(E4) is a leaving group; R^(E5) is halogen; R^(E6) is hydrogen,substituted or unsubstituted C₁₋₆ alkyl, or a nitrogen protecting group;each instance of Y is independently O, S, or NR^(E7), wherein R^(E7) ishydrogen, substituted or unsubstituted C₁₋₆ alkyl, or a nitrogenprotecting group; a is 1 or 2; and each instance of z is independently0, 1, 2, 3, 4, 5, or 6, as valency permits.
 3. The compound of claim 1,wherein the compound is of Formula (II) or (III):


4. (canceled)
 5. The compound of claim 1, wherein the compound is offormula:


6. The compound of claim 1, wherein the compound is of formula:


7. The compound of claim 1, wherein the compound is of formula:


8. The compound of claim 1, wherein the compound is of formula:


9. The compound of claim 1, wherein the compound is of formula:


10. The compound of claim 1, wherein the compound is of formula:


11. The compound of claim 1, wherein the compound is of formula:


12. The compound of claim 1, wherein the compound is of formula:


13. The compound of claim 1, wherein the compound is of formula:


14. The compound of claim 1, wherein the compound is of formula:

15-54. (canceled)
 55. The compound of claim 1, wherein the compound isof formula:

or a pharmaceutically acceptable salt, stereoisomer, or tautomerthereof.
 56. The compound of claim 1, wherein the compound is offormula:

or a pharmaceutically acceptable salt, stereoisomer, or tautomerthereof.
 57. A pharmaceutical composition comprising a compound of claim1, or a pharmaceutically acceptable salt thereof, and optionally apharmaceutically acceptable excipient.
 58. (canceled)
 59. A method oftreating a proliferative disease in a subject in need thereof, themethod comprising administering to the subject a therapeuticallyeffective amount of a compound of claim 1, or a pharmaceuticallyacceptable salt thereof. 60-91. (canceled)
 92. A method of inhibitingthe activity of a cyclin-dependent kinase (CDK) in a biological sampleor subject, the method comprising administering to the subject orcontacting the biological sample with a therapeutically effective amountof a compound of claim 1, or a pharmaceutically acceptable salt thereof.93-94. (canceled)
 95. A method of inhibiting transcription in abiological sample or subject, the method comprising: administering tothe subject or contacting the biological sample with a therapeuticallyeffective amount of a compound of claim 1, or a pharmaceuticallyacceptable salt thereof.
 96. (canceled)
 97. A method of inhibiting cellgrowth in a biological sample or subject, the method comprising:administering to the subject or contacting the biological sample with atherapeutically effective amount of a compound of claim 1, or apharmaceutically acceptable salt thereof. 98-105. (canceled)